[BioC] Help with justRMA in affy package

[James MacDonald]

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.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "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
package.

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

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

Thank you,
Chris Park

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