[BioC] cutoff for NUSE plot in oligo

Richard Friedman friedman at cancercenter.columbia.edu
Thu Mar 1 00:46:17 CET 2012

Dear list,

	As I had mentioned in an earlier post the NUSE plots for
Affy ST1.0 Gene chips are highly asymmetric and indeed
appear to be all positive. Empirically, I have found that
four older chips such as mouse 430.2
NUSE boxes which extend over 1.05 are suspect.
For an ST1.0 Genes analysis, I have 2 arrays with NUSE plots over 1.05.
Is this indicative of a need for rejecting the array?

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

"You can do a minuet to a mazurka
if you try hard enough but it will look

Judith Friedman, age withheld by request

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