Hi, I am studying RNAseq data obtained from human intestinal organoids treated with parasites derived material, so i have three biological replicates per condition (3 controls and 3 treated). I have performed reads count and normalization, and after DeSeq2 run with default parameters (padj<0.1 and FC>1), among over 16K transcripts included in the list of usable material, only 7 genes appear to be differentially expressed in term of padj value <0.05 (if i look at the pvalue not adjusted after correction for multiple testing, significant transcripts are arounf 600).
I can understand that maybe the treatment with parasites derived material may have not caused any crucial large significant changes in expression of genes, however i was wondering if i am missing something just because of the default parameters i have used as a threshold). Could you give please some advise on how to modify such parameters? I can imagine that if i change FC in a more stringent way, even less transcripts may appear to be significantly differentially expressed, however an opinion from experts may of course be of great help. Thanks in advance, SC