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?
1 answer
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.
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