Hi all,

I am interested in investigating differentially expressed genes, un-expressed genes and unchanged (same as control) genes among four samples (three replicates each) let's say A, B, C and D. I carried out an DEG analysis by taking A as control and calculated all fold change values w.r.t the control sample A. Now I am interested in finding those genes which are up or down regulated in sample D (w.r.t sample A) but unchanged in C (w.r.t sample A) and so on. Is there any tool which could let me know the unchanged genes with high confidence with FDR p-values? Or the NA values shown in DeSeq2 could be taken as unchanged expression? Mapped number of reads could give me an idea but I am more interested in having certain statistical significant values.

I appreciate your reply!

Best

Rahul