Hey everyone,

Kind of a dumb question but I use edgeR to do my differential gene expression. For some of our genes we want to show them as boxplots between our two different groups i.e control vs treatment

Do I just use logTMM values to draw the boxplot and use p values from edegR, if yes should they be simple p-values or adjusted p-values Or do I just run a t-test again on the gene of interest on the logTMM counts

Would appreciate any help. Thank You