Question: Interpreting heatmap in DESEQ2
gravatar for haitrieuphan82
9 months ago by
haitrieuphan820 wrote:

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 ? Does it represent expression level ? Thanks for your help


ADD COMMENTlink modified 9 months ago by casey.rimland100 • written 9 months ago by haitrieuphan820
gravatar for casey.rimland
9 months ago by
University of Cambridge, National Institutes of Health, Chapel Hill School of Medicine
casey.rimland100 wrote:

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:

Hope this helps a bit!

ADD COMMENTlink written 9 months ago by casey.rimland100

Thank you Casey

ADD REPLYlink written 8 months ago by haitrieuphan820

No problem, it was kinda cool to realize I actually knew something for once :D!

ADD REPLYlink written 8 months ago by casey.rimland100
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