Interpreting heatmap in DESEQ2 Entering edit mode 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 linkhttps://imgur.com/a/6oHgv ? Does it represent expression level ? Thanks for your help ADD COMMENT • link updated 6.1 years ago by casey.rimland ▴ 150 • written 6.1 years ago by haitrieuphan82 • 0 3 Entering edit mode casey.rimland ▴ 150 @caseyrimland-14915 Last seen 5.7 years ago University of Cambridge, National Insti… 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 COMMENT • link 6.1 years ago casey.rimland ▴ 150 2 Entering edit mode No problem, it was kinda cool to realize I actually knew something for once :D! ADD REPLY • link 6.1 years ago casey.rimland ▴ 150 
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