[BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS

Richard Friedman friedman at cancercenter.columbia.edu
Fri Nov 4 15:26:17 CET 2011

On Nov 2, 2011, at 10:16 AM, Vincent Carey wrote:

> you can read about formally calibrated outlier assessment for  
> microarrays in
> http://bioinformatics.oxfordjournals.org/content/25/1/48

Dear Vincent and List,

	I read your paper with great interest. i will implement it for  
datasets for Affymetrix Chips with
mismatch probes, to which it is geared, along with the weighting  
method suggested by Jim MacDonald, for arrays which pass the test.  
However a Gene ST1.0 dataset has come up with this kind of rejection  
question. Has you method be adapted to Gene ST1.0 arrays? If not, do  
you know of
a method analogous to yours which can be used for ST1.0s.

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
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

I am a Bayesian. When I see a multiple-choice question on a test and I  
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14

> On Wed, Nov 2, 2011 at 10:04 AM, Richard Friedman <friedman at cancercenter.columbia.edu 
> > wrote:
> Dear Bioconductor List,
>        Does anyone know of an objective criterion for the  
> identification of outlying arrays
> by pca?
>        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.


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