I am using the DESeq2 command variance stabilizing transformation to normalise raw read counts across 4 RNA-Seq experiments. Once normalised I will use these VST counts in Matrix eQTL, however I am having an issue with VST.
After carrying out VST, some of my results are genes have higher VST values than others which had higher raw read counts, i.e. re-ranking has occurred for some samples. Would anyone be able to shed some light on why this might have happened?