[BioC] Reg: PCA in bioconductor

[Richard Pearson]

Hi Rohit

You might also want to try 'pumaPCA' from the 'puma' package. It works on an 
'ExpressionSet' object created using mmgmos (also in puma). This allows you to use 
uncertainty information as well as point estimates of expression levels, and can be 
helpful in many situations. It is more compute intensive than prcomp or princomp though!

See puma vignette for further details

Cheers

Richard


Cristobal Fresno Rodríguez wrote:
> Rohit, I would try ?prcomp or ?princomp from the stats package.
> Hope it works for you,
> Cristobal
> 
> 2010/4/14 Rohit Farmer <rohit.farmer at gmail.com>
> 
>> Hello everyone ...
>>
>> I am using affymetrix data and want to do PCA using bioconductor ...
>> is there any package or library available which i can use to perform
>> the same ...
>>
>> Thanks
>>
>> Rohit
>>
>> --
>> Rohit Farmer
>> M.Tech Bioinformatics
>> Department of Computational Biology and Bioinformatics
>> Jacob School of Biengineering and Biotechnology
>> Sam Higginbottom Institute of Agriculture, Technology and Sciences
>> (Formerly known as Allahabad Agricultural Institute - Deemed University)
>> Allahabad, UP, INDIA - 211 007
>> Ph. No. 9839845093, 9415261403
>> e-Mail rohit.farmer at gmail.com
>> Blog http://rohitsspace.blogspot.com
>>
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-- 
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
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