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

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@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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor