I have two groups of RNAseq data, each group have 5 samples. I suspected that drug treatment would increase the overall expression variances in some pathways. So, I planned to compare all gene expression variances in that pathway or even in the top 500 expressed genes. I could calculate the variance from DEseq2 normalized counts, or variance stabilization transformed counts (vst or rld). The question is: which one should I choose? Does the VST process affect the signal I want to analyze?
Thanks and best regards,