vsd values vs normalized counts in DESeq2
Hi all!,
I know my question is a bit silly but wondering what major difference I might encounter if I use the VSD values of DESeq2 instead of the normalized counts(counts(dds, normalized = TRUE) for my heatmap? Best, Amare
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Kevin Blighe
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adR
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Normalised 'counts' will be positive only, and will follow a negative binomial distribution.
Variance stabilised expression levels will follow a distribution more approaching normality - think logged data.
For heatmaps, you then need to take consideration of:
- distance metric used
- colour scale
- breaks for colour scale
Kevin
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