[BioC] objective criterion for identification of outlying arrays by pca

shirley0818 shirley0818 at gmail.com
Sat Nov 5 16:29:35 CET 2011

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-----Original Message-----
From: Kevin R. Coombes <kevin.r.coombes at gmail.com>
Sent: 2011年11月4日 12:32
To: Richard Friedman <friedman at cancercenter.columbia.edu>
Cc: Bioconductor mailing list <bioconductor at r-project.org>
Subject: Re: [BioC] objective criterion for identification of outlying arrays by pca


I did say it was a long time ago; but it was *so* long ago that I had 
forgotten that we did that analysis in MATLAB....  We have used the idea 
several times since then, so I tracked down the R code and put together 
an example for you.  (See the attached PDF file.) The only thing you 
need is the "mahalanobis" function included in the Sweave script that is 
attached.  As long as you have a routine that produces a "scores" slot 
when computing principal components, this function should work.

To actually run the script, you need the "ClassDiscovery" package from 
our OOMPA suite of packages, since that contains our implementation of 
PCA (in the SamplePCA function).  You can install this from the R 
repository at
by following the instructions at


On 11/4/2011 8:48 AM, Richard Friedman wrote:
> Dear Kevin and List,
>     I read your paper with great interest but from the paper the 
> method seems to be implemented
> mainly in Matlab. I am not a Matlab user,  Is there a user-friendly R 
> version that can be used
> with no more R-scripting on the part of the user than is typical of 
> most bioconductor
> packages?
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
> I am a Bayesian. When I see a multiple-choi

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