Hi all,

I am interested in investigating clustering of samples using heatmap.2 in this paper “BioC2014: RNA-Seq workflow for differential gene expression”. However, I find it difficult to explain the Row Z-Score from the link https://imgur.com/a/6oHgv ? Does it represent expression level ? Thanks for your help

Row Z-Score is a scaling method for visualization in heat maps that helps enhance clusters of genes with similar trends in expression between samples.

Z-Score is calculated by:

(Gene expression value in sample of interest) - (Mean expression across all samples) / Standard Deviation

In the heat map you show, genes with dark red are upregulated and blue downregulated. However, since the rows are Z-Score scaled, you only have information about the a single genes varying expression across the samples. Comparing the color between two separate genes cannot tell you if Gene A is more highly expressed than Gene B, however heat maps are usually not used for this purpose and instead are meant to highlight differences between samples. 

This is also a previous post that is also a good explainer: https://www.biostars.org/p/159397/

Hope this helps a bit!