[BioC] DESeq2, plotting residuals vs.fitted values

[Michael Love]

On the scale of the counts, the fitted values are: assays(dds)[["mu"]]

to get the fitted values on the common scale, you just need to divide
each column by the size factor:

fitted.common.scale = t( t( assays(dds)[["mu"]] ) / sizeFactors(dds) )

So then the residuals are

counts(dds, normalized=TRUE) - fitted.common.scale



On Thu, Jul 17, 2014 at 10:49 AM, Mike Miller <mike.bioc32 at gmail.com> wrote:
> Dear All,
>
>
> I would like to plot residuals vs. fitted values for some of the candidate
> genes, after fitting the model and testing with DESeq2 package.
> Can someone tell me how I could extract the computed residuals and the
> fitted values per gene?
>
> Thank you in advance!
>
> Best,
> Mike
>
>         [[alternative HTML version deleted]]
>
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