Hi,

I have been using the DESeq2 package in R for differential expression analysis. I tried using LFC shrinkage using the lfcShrink function, but no matter what type of shrinkage estimator I give (normal/apeglm/ashr) I get the same results. Also - I get NA values in the padj column. Could this have to do with the number of samples expressing a certain gene? Can anyone help me understand what is going on?

Thank you

In ?lfcShrink we note that the output of the function is "a DESeqResults object with the log2FoldChange and lfcSE columns replaced with shrunken LFC and SE". So the p-value is not replaced.

We also have a FAQ in the vignette for your second question:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na