Entering edit mode
2.5 years ago
mgranada3
▴
60
I have this heatmap which represents 4 conditions and 5 timepoints each. I understand that when I use z-score the legend refers to the standard deviations. However, when you're not using z-scores what do those values represent? It says 0 to 20, but of what? What would 20 be? 20 transcripts? 20,000 transcripts? 20 FPKM?
I have checked the vignette but I am not finding the answer to my question.
My organism has ~5.5k genes.
Can you show us the code you're using to generate the heatmap? I don't think DESeq2 plots FPKM - it must be one of either raw counts or normalized counts.
My count matrix was made using featureCounts and I read this into DESeq2.
I don't know how much code you need but this is just the heatmap:
Well you're clearly plotting assay(vsd) so what's that?