hello, I'm sorry if the question may seem trivial but I am a beginner in this field. I have a dual microarray and I have calculated the Z-scores for each gene, I have to find the ones differentially expressed . Is it correct if I get the corresponding p-values and use a volcano plot to decide the cut-off value? are there any other steps I should do? (I've already done the correction and normalization steps). If the microarray slides were two, would this method still be correct?
Please check out the
limma package and read the manual. Follow the suggested workflow and choose genes with an adjusted p-value below 0.05. This is how one typically analyzes microarrays. 0.05 is a common and accepted cutoff. Z-scores can later be helpful for visualization as they indicate how much a value differs from a group mean but for differential analysis one (by best knowledge) typically does not use them in the gene expression world.