hi, Im doing a mas5 normalization & I have a technical question: using mas5() i get the normalization values foreach probeSet foreach chip using mas5calls() i get PMA calls oreach probeSet foreach chip how i can have all in the same file, foreach probeset foreach chip 1 column of PMA values followed by a column of normalized values? (can i use a particular method for that like mas5.detection() or mas5calls,AffyBatch-method() or mas5calls,ProbeSet-method() or mas5calls.AffyBatch() or mas5calls.ProbeSet() )

Hi Enrique, D.Enrique ESCOBAR ESPINOZA wrote: > hi, > > Im doing a mas5 normalization & I have a technical question: > using mas5() i get the normalization values foreach probeSet foreach > chip > using mas5calls() i get PMA calls oreach probeSet foreach chip > > how i can have all in the same file, foreach probeset foreach chip 1 > column of PMA values followed by a column of normalized values? > (can i use a particular method for that like mas5.detection() or > mas5calls,AffyBatch-method() or mas5calls,ProbeSet-method() or > mas5calls.AffyBatch() or mas5calls.ProbeSet() ) biocLite("affycoretools") affystart(plot=FALSE, express="mas5") will output a text file formatted just as you request. If you want to do anything else with that file, you can read it into R using read.table(). Best, Jim > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.