[BioC] request

[Laurent Gatto]

On 6 August 2013 16:32, Wolfgang Huber <whuber at embl.de> wrote:
> @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value.

I have a similar function (pRoloc::plot2D) that invisibly returns the
prcomp(...)$x[, dims] matrix that used for plotting, where dims are
the PCs requested by the user (default being 1:2). I also report the
proportion of variance explained by these two components on the axes.

Best wishes,

Laurent

> Best wishes
>         Wolfgang
>
>
>
> On 6 Aug 2013, at 08:54, Alexey Moskalev <amoskalev at list.ru> wrote:
>
>> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq?
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-- 
Laurent Gatto
- http://proteome.sysbiol.cam.ac.uk/lgatto/
Cambridge Centre for Proteomics
- http://www.bio.cam.ac.uk/proteomics
Using R/Bioconductor for proteomics data analysis
- http://lgatto.github.io/RforProteomics/