ITADN

dataset count distribution column was deprecated [R]

#1450Openmyushen 创建于 2025-12-16
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myushencommented
Hi, I am trying to get raw counts from Census API, but for some datasets the values do not appear to be raw counts. I think there was a column x_approximate_distribution in CELLxGENE could be used to infer the underlying data distribution, but this field has been deprecated. I was wondering whether there is another column in the schema that serves a similar purpose, or whether I might be overlooking an existing annotation that indicates whether the counts are truly raw. An example dataset reprex: library(cellxgene.census) system("aws s3 cp --no-sign-request s3://cellxgene-census-public-us-west-2/cell-census/2024-07-01/h5ads/218acb0f-9f2f-4f76-b90b-15a4b7c7f629.h5ad ~/scratch/cache_temp") x = zellkonverter::readH5AD("~/scratch/cache_temp/218acb0f-9f2f-4f76-b90b-15a4b7c7f629.h5ad", reader="R", use_hdf5 = T) x = x[, colData(x)$donor_id == "1221"] assay_mat <- SummarizedExperiment::assay(x, "X") assay_mat |> colSums() |> summary() Min. 1st Qu. Median Mean 3rd Qu. Max. -201.990 -58.328 -2.493 -4.936 44.135 263.616 assay_mat |> as.numeric() |> summary() Min. 1st Qu. Median Mean 3rd Qu. Max. -5.3557138 0.0000000 0.0000000 -0.0001599 0.0000000 10.0000000
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