I'm working on a,RNA-Seq data analysis, whose experimental plan is as follows:
sample phenotype traitement
3 X Col control normal
3 X Col_HS control heat-shock
3 X mutant mutant normal
3 X mutant_HS mutant heat-shock
The main objectif is to discover the effect of the mutation on the transcription and the analyse control vs heat-shock serves me as a control for the quality of the analyzes because the effects of heat-stress have been well studied. However I don't know which approach used to validate my analysis. I retrieved a list of 12 genes experimentally validated as differentially expressed in heat-shock, and I looked if I found them in my experience. I find 9 of 12 but as I have more than 1000 differentially expressed genes I don't know if it's good or not. My question is, how do you judge the pertinence of an analysis? I try different tools and I would like to make a comparison of these tools to choose the best. How can I do ?