[BioC] Help with justRMA in affy package

James MacDonald jmacdon at med.umich.edu
Tue Apr 13 14:44:05 CEST 2004

Neither rma nor justRMA will do a PM-MM model. If you are interested in
PM-MM type analyses, you will have to use expresso(). See ?expresso for
more information.



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

>>> "PARK,CHRISTOPHER CHANGSUN" <ccpark at ucla.edu> 04/12/04 04:37PM >>>

Hi all,

I am a newcomer to the analysis of microarray data, and I was looking
to do
a comparison of of normalization methods using the Bioconductor affy

I 'd like to perform the function justRMA on my dataset.  Does anyone
if this method takes into account perfect match values only, or does
consider perfect match - mismatch values.

I would like to perform just RMA with both perfect match only and
match - mismatch data.  Could someone give me some advice on how to do

Thank you,
Chris Park

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