I performed a deseq analysis on my samples (11 controls and 33 experimental samples). It is true that there are huge variations within each group, but although the pval are very low, the padj are always 1. Plus when I put in the command:
resSig = res[ res$padj <.05,]
the list that it gives me includes all the transcripts although the padj are 1.
I would really appreciate any advice or help. Thanx in advance.