[BioC] DESeq - plotPCA

Wolfgang Huber whuber at embl.de
Thu Mar 7 23:01:10 CET 2013

Il giorno Mar 6, 2013, alle ore 4:16 PM, Simon Anders <anders at embl.de> ha scritto:
> For (i), it does not make much difference whether you use all data or only highly variable genes, as genes with low variance across samples provide only little information on sample distances anyway and so have little influence on the result.

In fact, the data from genes with low overall variability (which tends to coincide with low mean count) may be relatively more dominated by batch effects (if present), and thousands of such genes in a PCA might overwhelm the more interesting biological signal visible in the more highly detectable genes.

	Best wishes

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