Heatmap methodology

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Mathew Baldwin

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May 25, 2020, 2:11:37 PM5/25/20
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Hi, 

Just wondering if anyone would be able to tell me how the heat maps on the software are calculated? I have looked at the source code, but it is beyond me.

Specifically, what is input in the Heatmap is it the rlog of the counts matrix, a variance stabilised transformation or something else entirely?

cheers, 

Mat


Ivo Kwee

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May 26, 2020, 11:35:41 AM5/26/20
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Hi Mathew. 

We use the quantile normalized log(1+CPM) for the heatmaps and  in downstream analysis for example for Limma. The rlog and VST of the count matrix is more specific for Deseq2 and the normalized logCPM is more algorithm "neutral". If you are interested, the relevant computation part is in the file 'ngs-fit.r' from line 61-82.

Ivo
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