Hi dear all, I am trying to compare my RNA-seq data sets.how can I compare expression profile between groups as following: Case treated, Case untreated, Control treated, Control untreated. The p value <0.05 and fold change>2 of each comparison are not as the same and I miss my target genes when I filter each group.For example p val of TGF b1 in case treated vs. Case untreated group is 0.04 but in control treated vs.control untreated group id 0.1 and almost p value of the genes obtained in case treated vs.case untreated are different from control treated vs. Control untreated. Is it possible to select only one comparison for example case treated vs. control untreated and all following analysis perform on that?what is the main way to select an influenced gene after treatment? I want to select 3 target genes involved in a particular signaling pathway for qRT-PCR validation, but p value of each comparison is not as the same and I am confused . I would be so appreciated if you help me. Thanks