Hi I'm not particulary familiar with any of the affy functions in bioconductor i'm under the impression that all of the affy functions are based on using PM & MM values for any analysis..... BUT The Custom affy chip we have doesn't have Mismatches I'd like to use Bioconductor only using the PM values from the CEL file & was wondering if this is possible at all in bioconductor... If so can some suggest what functions need to be used We can extract seperately Normalised expression values Background No of probes Gene Names P-Values but would prefer to be able to use the CEL file directly and preferably the raw data Cheers Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

Some of the affy functions use the MM values and some do not. AFAIK, RMA and playerout do not use MM values, whereas you can use either PM or PM-MM for li.wong, and of course MAS and avgdiff use MM values. HTH, 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 >>> Jason Skelton <jps@sanger.ac.uk> 10/22/03 11:30AM >>> Hi I'm not particulary familiar with any of the affy functions in bioconductor i'm under the impression that all of the affy functions are based on using PM & MM values for any analysis..... BUT The Custom affy chip we have doesn't have Mismatches I'd like to use Bioconductor only using the PM values from the CEL file & was wondering if this is possible at all in bioconductor... If so can some suggest what functions need to be used We can extract seperately Normalised expression values Background No of probes Gene Names P-Values but would prefer to be able to use the CEL file directly and preferably the raw data Cheers Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor