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

James W. MacDonald jmacdon at med.umich.edu
Wed Nov 2 15:11:32 CET 2011

Hi Rich,

On 11/2/2011 10:04 AM, Richard Friedman wrote:
> Dear Bioconductor List,
>     Does anyone know of an objective criterion for the identification 
> of outlying arrays
> by pca?

I don't know an objective criterion for this. However, unless the 
'outlier' is ridiculously bad, you might be better off using array 
weights to down-weight the offending array(s). In limma, the 
arrayWeights() and arrayWeightsSimple() functions allow you to generate 
weights that you can then feed into lmFit().



>     I usually do this subjectively. However the experimental 
> investigator whom I am helping
> has a different subjective sense than I do, so that I wonder if there 
> is a hard-and-fast criterion.
> 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-choice question on a test and I 
> don't
> know the answer I say "eeney-meaney-miney-moe".
> Rose Friedman, Age 14
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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