Question: CAMERA fold changes per gene set?
gravatar for chris86
9 weeks ago by
UCL, United Kingdom
chris86370 wrote:

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?

Best wishes,


ADD COMMENTlink written 9 weeks ago by chris86370
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 231 users visited in the last hour