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Old 04-30-2014, 11:11 AM   #8
Wolfgang Huber
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Location: Heidelberg, Germany

Join Date: Aug 2009
Posts: 109

Originally Posted by moritzhess View Post
As far as I know, you have to tell DESEQ to treat all expression values as if they were emerging from a single condition by specifying method="blind" when extimating the Dispersions.
Yes. And depending on the data, there may not always be a variance stabilising transformation. In particular, the error model on which the transformation is based assumes that for most genes the variance is dominated by technical noise and natural biological variation between replicates, and that the effects of true differential expression affect only a minority of genes. If that is not the case, then the whole concept does not really work.

As Mike Love says, the variance stabilsing transformation tends to be misled in cases when the size factors strongly vary between samples, and (at least) in these case the rlog transformation is preferable.
Wolfgang Huber

Last edited by Wolfgang Huber; 04-30-2014 at 11:16 AM.
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