I am using DESeq2 to analyze my RNAseq data and really like the package. There is lots of information available, a very helping community, and the code is quite easy. However, I do seem to have one problem when it comes to my normalized read counts. It seems that four of my samples are not properly normalized (i.e., the 3 controls at 28 hrs and one of the mocks at 28 hrs, see figure) and this clearly shows in the analysis afterwards. I gather this from the boxplots of the normalized read counts for each gene per sample that I attached. Am I wrong to make this conclusion based on this plot? And if not, what do I do about it?
Thank you for your time. Hopefully someone here can help me.