Sorry for this naive question, but I am new to principal component analyses and how to display them. I have two different gene sets, coding and non-coding genes, and count data from two different conditions (four replicates of both). I want to compare how the samples cluster in the two gene sets, i.e. do they have the same expression signatures. I made PCAplots of each gene set separately in DESeq2, but I wonder if it makes sense at all to plot them in the same PCA-plot?

Thanks, Jon

You could plot PC1 from gene set 1 against PC1 from gene set 2. Or alternatively rbind the two matrices (genes in set x samples) and use a heatmap with row colors and do manually row ordering (see pheatmap in our workflow).

I would use rlog, VST or log(normalized counts + pseudocount).