I’m running an RNA seq analysis. When I use limma-voom I get an error only when I use I select the gene annotation add file option. If I don’t use the gene annotation option, my analysis runs fine with geneIDs as the output. I’ve been using a BED file specific for GRCH38 since I’ve aligned my transcriptome to this particular build… I downloaded this file from the table output on UCSC. Does anyone else know what gene annotation file type is supported by limma-voom? Or better yet, can anyone recommend a gene annotation file for grch38 that works for them?
My error message is ‘Error in make.u’.