Search
Question: Interpreting heatmap in DESEQ2
0
gravatar for haitrieuphan82
4 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 https://imgur.com/a/6oHgv ? Does it represent expression level ? Thanks for your help

 

ADD COMMENTlink modified 4 months ago by casey.rimland80 • written 4 months ago by haitrieuphan820
2
gravatar for casey.rimland
4 months ago by
University of Cambridge, National Institutes of Health, Chapel Hill School of Medicine
casey.rimland80 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: https://www.biostars.org/p/159397/

Hope this helps a bit!

ADD COMMENTlink written 4 months ago by casey.rimland80

Thank you Casey

ADD REPLYlink written 4 months ago by haitrieuphan820
2

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

ADD REPLYlink written 4 months ago by casey.rimland80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 262 users visited in the last hour