[BioC] what normalization method does mas5 use

James MacDonald jmacdon at med.umich.edu
Wed Jul 14 21:22:14 CEST 2004

The mas5 algorithm scales the data to have the same mean (500 is the
default). This corresponds to what Affy has published in their
documentation. You can look at the code by typing
affy.scalevalue.exprSet at an R prompt, or look at the man page by
prepending that with a ?.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Brian Bennett <brianb00 at gwu.edu> 07/14/04 02:26PM >>>

I'm using the affy spike-in latin square data to try to determine which
summarization technique is the best.  I was wondering if anyone new what
normalization technique mas5 uses in BioConductor.  I have been using
quantiles for rma, dChip, plier, and gcrma.  I just used the mas5()
command to normalize and summarize without considering its technique.  I
have to go back and renormalize and resummarize if quantile
normalization is not its default normalization method in order to yield
more consistant data.

Thank you,
Brian Bennett

brianb00 at gwu.edu 

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