Dear List,



I may be wrong here, but I wanted to know if the output of DE calling would differ if the normalised count were to be used rather than the raw counts as is the current case (using the cds - countDataSet)?



As in the vignette, when trying to plot the heatmap, you rather use the vsd object (as you mention it is better for visual purposes). I was wondering if it would affect the DE calling? Or perhaps it does not matter because the baseMeans are calculated by dividing by the sizeFactors, as in a way it is normalised?



I am using R 2.13 and its DESeq version and not the developmental versions.





Many Thanks,

Natasha


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