Run SpaNorm spatial normalization

Normalize spatial transcriptomics counts with the optional Bioconductor SpaNorm backend and store the normalized expression in a new Seurat assay.

Usage

RunSpaNorm(
  srt,
  assay = NULL,
  layer = "counts",
  image = NULL,
  coord.cols = c("col", "row"),
  new_assay = "SpaNorm",
  tool_name = "SpaNorm",
  store_results = TRUE,
  store_spe = FALSE,
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

layer

Assay layer used for expression values.

image

Name of the Seurat spatial image used by the spatial workflow. If NULL, the first image is used when present.

coord.cols

Metadata coordinate columns used by the spatial workflow when no image is available.

new_assay

Name of the assay used to store SpaNorm-normalized data.

tool_name

Name used to store detailed SpaNorm results in srt@tools.

store_results

Whether to store the full result in srt@tools.

store_spe

Whether to store the backend SpatialExperiment returned by SpaNorm.

verbose

Whether to print the message. Default is TRUE.

...

Additional arguments passed to SpaNorm::SpaNorm(), such as sample.p.

Value

A Seurat object with SpaNorm-normalized expression stored in new_assay. When store_results = TRUE, parameters, coordinates, features, cells, and optional backend output are stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)

SpatialSpotPlot(
  spatial,
  features = rownames(spatial)[1:2],
  assay = "Spatial",
  layer = "data",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


if (
  requireNamespace("SpaNorm", quietly = TRUE) &&
    requireNamespace("SpatialExperiment", quietly = TRUE)
) {
  spatial <- RunSpaNorm(
    spatial,
    assay = "Spatial",
    layer = "counts",
    coord.cols = c("x", "y"),
    new_assay = "SpaNorm",
    store_spe = FALSE,
    sample.p = 0.25,
    verbose = FALSE
  )

  SpatialSpotPlot(
    spatial,
    features = rownames(spatial[["SpaNorm"]])[1:2],
    assay = "SpaNorm",
    layer = "data",
    overlay_image = FALSE,
    coord.cols = c("x", "y")
  )
}
#> (1/2) Fitting SpaNorm model
#> 496 cells/spots sampled to fit model
#> Downloading uv...
#> Done!
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, log-likelihood: -2958360.662778
#> iter:  1, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  1, log-likelihood: -2958360.662778
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  2, log-likelihood: -2495300.394335
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  3, log-likelihood: -2405264.343231
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  4, log-likelihood: -2372696.784295
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  5, log-likelihood: -2355309.660312
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  6, log-likelihood: -2347317.178076
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  7, log-likelihood: -2343650.575070
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  8, log-likelihood: -2341824.206008
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  9, log-likelihood: -2340907.816825
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 10, log-likelihood: -2340375.215169
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 11, log-likelihood: -2340088.154363
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 12, log-likelihood: -2339892.368043 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, log-likelihood: -2326881.317180
#> iter:  2, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  1, log-likelihood: -2326881.317180
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  2, log-likelihood: -2324189.878018
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  3, log-likelihood: -2324065.063435 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, log-likelihood: -2323987.090719
#> iter:  3, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  1, log-likelihood: -2323987.090719
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  2, log-likelihood: -2323791.451205
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  3, log-likelihood: -2323752.772324 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, log-likelihood: -2323673.478839
#> iter:  4, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  1, log-likelihood: -2323673.478839
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  2, log-likelihood: -2323636.663335
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  3, log-likelihood: -2323612.205743 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  5, log-likelihood: -2323612.205743 (converged)
#> (2/2) Normalising data