Hello, I'm having a hard time figuring out how limma can switch the sign of an effect compared to the raw cpm or log2(cpm) values. In the figure below, I'm showing 4 genes (2x2 matrix) in our data compared between two conditions (called infected and control for simplicity). On the top row, cpm and voom normalized data agree as I would expect. However, on the bottom, there appear to be pretty substantial differences.
Thanks for any insight you can add into this! I've already checked all the usual suspects like whether any of the labels are different, and I haven't found an explanation as to why an effect would switch sign (I get how an effect may become more/less evidence). Thanks!