Dear all, I have a question. It is better to perform this analysis using CPM or TPM values? Other times I performed this analysis using TPM. This time I have the replicate values only for CPM, while for TPM I have only the mean for each condition. Which is the best way?
Which tool are you using? When I use FGSEA, I pass in a differential-expression summary statistic, rather than values from individual samples. For a given gene, the statistic I use is (-log10 of unadjusted p-value) * (sign of differential expression coefficient).
As others have mentioned TPM is generally better - however the choice may be tool-specific.
For example, you cannot use TPM normalised counts for differential gene expression analysis with EdgeR.