[BioC] edgeR MDS

[Gordon K Smyth]

Dear Manoj,

Anything is possible.  Just output logCPM:

  y <- cpm(dge, log=TRUE, prior.count=3)

Then make whatever plot you like.  I've never made a 3d pca plot, but a 
few seconds of googling gives me:

  pc <- princomp(y)
  library(rgl)
  plot3d(pc$scores[,1:3])

Best wishes
Gordon

On Tue, 4 Jun 2013, Manoj Hariharan wrote:

> Dear Gordon,

> Thanks for your input on plotMDS.

> Can you please comment on the second question I had - is it possible to 
> use the DGEList object to make a 3D PCA plot?

> Thanks,
> Manoj.





________________________________
  From: Gordon K Smyth <smyth at wehi.EDU.AU>
To: Manoj Hariharan <h_manoj at yahoo.com> 
Cc: Bioconductor mailing list <bioconductor at r-project.org> 
Sent: Wednesday, May 22, 2013 4:53 PM
Subject: edgeR MDS


Dear Manoj,

plotMDS does not do PCA.  As the documentation says

"This function is a variation on the usual multdimensional scaling (or 
principle coordinate) plot".

Statisticians are sometimes not very imaginative when choosing names for 
things, but PCA is an abbreviation for "principle component analysis" 
which is not the same as "principle coordinate analysis".

Best wishes
Gordon

> Date: Tue, 21 May 2013 11:55:36 -0700 (PDT)
> From: Manoj Hariharan <h_manoj at yahoo.com>
> To: "Bioconductor at r-project.org" <Bioconductor at r-project.org>
> Subject: [BioC] edgeR MDS
>
> Hello,
>
> I am working on edgeR version 3.2.3.
>
>> From the documentation, I guess the "plotMDS.DGEList" is similar to 
>> PCA. The manual mentions that "Distances on the plot represent 
>> coefficient of variation of expression between samples".
>
> Is it possible to get a value of proportion of variance explained from 
> each dimension (component)? Also, is it possible to use the DGEList to 
> make a 3D PCA plot?
>
> Thanks,
>
> Manoj.
>
>  
> Manoj Hariharan
> Staff Researcher
> The Salk Institute for Biological Studies
> La Jolla, CA 92037
> Office: 858.453.4100 x2143

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