[BioC] DESeq2 plotPCA and scale

[Daniel Brewer (BIO)]

When trying to replicate the function of plotPCA using prcomp as I use normally I noticed that I could only get it to match if I set scale=F in prcomp().   When scale=T scaling is done by dividing the (centered) columns of x by their standard deviations i.e. the genes are given equal weight.  By standard I would set scale=T, but I was wondering whether it is appropriate in this situation or not?  Any thoughts?

Thanks

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Dr Daniel Brewer
Senior Bioinformatics Officer | Cancer Genetics
School of Biological Sciences | University of East Anglia | Norwich Research Park | Norwich | NR4 7TJ

Tel: +44 (0) 1603 592906 | Email: d.brewer at uea.ac.uk