I'm running CAMERA on one of my datasets with gene set collections imported from MSigDB and graphite, and I am getting NaN results for a large fraction of gene sets that I'm testing (around 50% of pathways for some collections). This is odd because I don't remember that happening a few versions ago the last time I used CAMERA on the same gene sets. I've prepared a test case that demonstrates the problem. You can download the script and data file from here: https://www.dropbox.com/sh/dp5aheqzvf2rij5/AADuA68Hk5BdRIJpL4H_knbHa?dl=0 Simply put them in the same folder and run the script, which is just this:
library(edgeR) testcase <- readRDS("camera-nan-testcase.RDS") result <- with(testcase, camera(dge, pathway, design, makeContrasts(contrasts=contrast, levels=design))) print(result)
The result should be:
Warning message: Zero sample variances detected, have been offset data.frame with 1 row and 4 columns NGenes Correlation Direction PValue <numeric> <numeric> <character> <numeric> set1 40 NaN Up NaN
I have no idea what's causing this. Is there something about this gene set that makes it incompatible with CAMERA, or is there an issue in my data?