objective criterion for identification of outlying arrays by pca
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shirley zhang ★ 1.0k
Last seen 7.1 years ago
Sent from my HTC Touch Pro2 on the Now Network from Sprint?. -----Original Message----- From: Kevin R. Coombes <kevin.r.coombes@gmail.com> Sent: 2011?11?4? 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 Hi, 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 http://bioinformatics.mdanderson.org/OOMPA by following the instructions at http://bioinformatics.mdanderson.org/Software/OOMPA Best, Kevin 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 [The entire original message is not included]
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