I have two groups with 12 (6 + 6) samples that were generated from bulk-RNA-Seq experiments. While performing the differential expression analysis the adjusted-p-value came out to be 1 with both DESEQ2 (Wald, LRT) and EdgeR (Quasi-likelihood, LRT). After, skimming through a few posts and papers, I found that its the result of Benjamini & Hochberg (BH) procedure and low replicate counts per group. Can anyone suggest some other workflow or library that I should implement to extract differentially expressed genes from such low biological replicates?
The workflows are called DESeq2 ad edgeR, they are perfectly fine for want you aim to do, getting results from low replicate number. If the results are not significant, then it is what it is. For a more elaborate answer please post code and results of
plotPCA, see the DESeq2 workflow for it, plus please some details what these samples are.