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Old 06-07-2016, 01:20 AM   #1
Location: Spain

Join Date: Nov 2013
Posts: 28
Default DESeq2 pheatmaps

Hi all,

I'm examining functions to create heatmaps so that I can show the expression pattern of the top of my differentially expressed genes list, but I am a bit confused about which data transformation is more suited to create an informative heatmap. I'm wondering if I should use a heatmap with a z-score scaling to represent differences in fold change or something recovered by the varianceStabilizingTransformation and pheatmap function provided in the DESeq2 package.

In case of using the functions provided within DESeq2, is it more suited to create a heatmap of log2 normalized counts, from regularized log transformation or from variance stabilizing transformation? What are the measurement units seen in the heatmap legends in the DESeq2 manual?

I would greatly appreciate any help or suggestions
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