[BioC] what normalization method does mas5 use

F Duan f.duan at yale.edu
Wed Jul 14 21:23:48 CEST 2004

Oh, no, mas5 assigns a scaling factor: default is 500.


-----Original Message-----
From: F Duan [mailto:f.duan at yale.edu] 
Sent: Wednesday, July 14, 2004 15:22
To: 'Brian Bennett'; 'bioconductor at stat.math.ethz.ch'
Subject: RE: [BioC] what normalization method does mas5 use

I believe it's also quantile if you use affy package.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Brian Bennett
Sent: Wednesday, July 14, 2004 14:26
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] what normalization method does mas5 use


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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