I have come across a weird problem. I a matrix of raw gene counts (RNASeq Level 3) and I have two groups - treated vs. untreated. I check the mean of raw counts in two groups, it is higher in the treated group. And then I take a log2 of the raw counts and check the mean in two groups again. I see the mean in treated group is smaller than in the untreated group.

I plotted the raw counts vs. log raw counts to see the distribution, the treated group has few points with large values whereas the untreated group has less outliers. I don't know what is causing the flip in means. Since log is a monotonic function, the mean in treated group should remain higher than the mean in untreated.

Has anyone faced a problem like this before?

Thank you.