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How to set n_genes in SCTransform #173

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SihanLiUVa opened this issue Nov 6, 2023 · 1 comment
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How to set n_genes in SCTransform #173

SihanLiUVa opened this issue Nov 6, 2023 · 1 comment

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@SihanLiUVa
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Hi! According to the issue#124, I am trying to increase the number of genes in the function SCTransform. Here are my codes:
group1 <- SCTransform(group1_data,vars.to.regress = "nCount_RNA", ncells = 5000, vst.flavor = "v2", return.only.var.genes = FALSE, n_genes = 5000)
I noticed that in the argument of this function, the n_genes is supposed to pass to sctransform::vst, where the n_genes is used. However, i still got this message from my console.
Get Negative Binomial regression parameters per gene
Using 2000 genes
Would you please teach me how to pass this argument? Thank you so much in advance!

@saketkc
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saketkc commented Nov 10, 2023

Duplicate of satijalab/seurat#7998

@saketkc saketkc marked this as a duplicate of satijalab/seurat#7998 Nov 10, 2023
@saketkc saketkc closed this as completed Nov 10, 2023
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