[BioC] what normalization method does mas5 use
f.duan at yale.edu
Wed Jul 14 21:23:48 CEST 2004
Oh, no, mas5 assigns a scaling factor: default is 500.
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.
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.
brianb00 at gwu.edu
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