I have a raw read count file of RNAseq normalized using TMM in edgeR. In addition to finding DEGs using edgeR, I was wondering if it is valid to compare the number of reads mapped to the gene of interest and the number of reads mapped to 'internal control' (eg. ubiquitin conjugating enzyme) as the relative expression level of the gene of interest?
Because I measured the relative expression level of those genes of interest using RT-PCR previously. I would like to see if RNA-seq data would support my previous RT-PCR data.
Any comments and thoughts are welcomed! And thank you in advance!