Dear bioconductor/ limma developers
I was wondering if there is a straightforward way of getting fold changes per gene set out when I run CAMERA or any of the gene set functions in limma. This is because I need to plot them. I am enjoying using the general pipeline, but at the moment to get the fold changes I am having to code it out manually.
Currently I am getting the log(TPMs) for every gene in the pathway, calculating the mean, then calculating a second mean per group. Next I divide one group value by the other.
Is this even the best way to approximate the fold change per pathway between groups?