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I am doing a differential gene expression analysis to find out genes that are differentially expressed in one cell type from the lung in two conditions, control and idipathic pulmonary fibrosis (IPF). In total I have 152538 cells. Can anyone help me provide a hint to understand why only NAs get returned for the pvalues and adjusted pvalues?

> table(seurat$group)

Control     IPF 
  64652   87886 

> degs <- FindMarkers(seurat, 
                            ident.1 = "IPF",
                            ident.2 = "Control")
> head(degs) 
         p_val  avg_logFC pct.1 pct.2 p_val_adj
SPP1        NA  1.2721607 0.390 0.125        NA
FN1         NA  1.1768771 0.741 0.409        NA
CRIP1       NA  1.0484934 0.938 0.832        NA
CCL18       NA  0.9830185 0.734 0.469        NA
S100A10     NA  0.5799861 0.965 0.902        NA
VIM         NA  0.5666287 0.992 0.964        NA
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  • $\begingroup$ are you showing the full function called? it should FindMarkers(seurat,group.by="group",ident.1="IPF",ident.2="Control") unless you set the identity to be group $\endgroup$
    – StupidWolf
    Jan 21 at 10:16
  • $\begingroup$ @StupidWolf Yes, I did set the identity to group. The function works for other cell types in the same data set. $\endgroup$
    – Charles
    Jan 22 at 11:54

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