Entering edit mode
3.1 years ago
charlesgwellem
▴
10
I am doing a differential gene expression analysis to find out genes that are differentially expressed in one cell type from the human 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?
> Idents(seurat) <- "group"
> 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