[BioC] Practical utilization of SQN in ST1.0 Gene normalization.

[Richard Friedman]

Dear Bioconductor List,

	I read Zhijin Wu and Martin Aryee's paper of subset Quantile  
normalization with great interest.
The method is implemented in a CRAN package SQN which requires the  
labeling of the negative control
probes. It is not clear to me how to identify those probes for the  
Affymetrix Gene ST1.0 chips.
It is also not clear to me how to integrate this step into the usual  
normalization workflow to replace
rma for the chip metioned above. As I understand it, SQN would only  
replace the quantile normalization
step, but not the background correction or summarization steps. How  
then can it be used for practical normalization
in oligo. I would appreciate any suggestions members of the list might  
have.

Thank you as always,
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