Hi everyone,

I'm interested in generating a gene clustering similar to the one in this workflow: RNA-seq workflow: gene-level exploratory analysis and differential expression (see "Gene Clustering" section 6.3)

I would like to do for the DESeq2 results only (ie the deferentially expressed genes determined by thresholds). So the end result would show the two groups that I've compared (eg. control and treatment) and the DEGs clustering.

Is it possible to make the heat map according to the log2fc differences? does it makes sense to represent it like that? or should I represent it with a the transformed data (ie vsd)

Best

You can do either (LFC or expression values), although i dont see the point of a heatmap with just one LFC. We have examples of both in the workflow. See “ We can now plot the log2 fold changes in a heatmap” in the time course section.