In addition to a classic differential expression analysis, I'd like to investigate the expression of pre-defined 'candidate genes' from my RNA-seq data.
What I've done: from a TMM-normalised transcript quantification matrix (the same kind of matrix that is leveraged by differential expression analysis by edgeR, voom, DESeq2 etc..), I pulled out the genes I was interested in and scaled/log-2 transformed the TMM counts to produce heatmaps that do show condition-specific expression patterns (but these didn't show up in the differential expression analysis). I frame it as an exploratory analysis, not as a definite differential expression analysis.
However, I can not find any published similar workflow. I tried various ways to google this question, and I could not find a single comment on such approach, which I find very surprising. Can anyone help by providing some sources or insights they have on this?