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Old 01-31-2017, 12:46 AM   #1
Location: UK

Join Date: Nov 2015
Posts: 19
Default Normalising heatmap counts

I'm trying to produce a heatmap for my RNAseq dataset (using RPKM values). The counts vary from 5 - 40 000+. Obviously when I produce the heatmap, using Pheatmap, the values are very skewed towards the top end (see photo).

Can anyone reccomend a good method of normalising / transforming the data to give a better visual representation?

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4galaxy7 is offline   Reply With Quote
Old 01-31-2017, 04:56 AM   #2
Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 97

Most commonly log scaling is used. Recommended is probably to use DESeq2 or similar to extract log normalized counts with a more sophisticated model than RPKM.
wdecoster is offline   Reply With Quote

bioinformatics analysis, heatmap, rnaseq

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