Thanks a lot Jim! This is working perfectly. You saved my day! Dmitry -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Thursday, April 06, 2006 4:06 PM To: Dmitry Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] pm() mm() functionality changed? Dmitry wrote: > Thank you, > > I tried this. The output is not exactly what I needed: > > 1007_s_at 649 371 > 1007_s_at.1 952 1043 > 1007_s_at.2 1640 2892 > 1007_s_at.3 3505 4894 > 1007_s_at.4 3703 2188 > 1007_s_at.6 2822 1812 > > Why should we re-create names for the rows whcih (names) are already there? > Is there any function which will allow to retrieve the whole line of PM and > MM values for several chips at once, with one row ID? > I used to loop through my: > > PM<-pm(Data) > MM<-mm(Data) > Cb<-cbind(PM,MM) OK, then how about gn <- geneNames(Data) PM <- pm(data, genenames = gn) MM <- mm(data, genenames = gn) Cb <- cbind(PM,MM) Jim > > and was happy till pm() and mm() stop working:-) > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Thursday, April 06, 2006 2:45 PM > To: Dmitry > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] pm() mm() functionality changed? > > Dmitry wrote: > >>Hi ALL, >> >>What happened to pm() and mm() functions? >>I'm running my old scripts: >> >>PM<-pm(Data) >>MM<-mm(Data) >>Cb<-cbind(PM,MM) >> >>And my Cb output looks like this: >> >>1 378 52 >>2 930 486 >>3 1424 463 >>4 93 47 >>5 248 83 >>6 314 122 >> >>But I need my old way with probe pair ids instead of indices: >> >>1007_s_at1 649 371 >>1007_s_at2 952 1043 >>1007_s_at3 1640 2892 >>1007_s_at4 3505 4894 >>1007_s_at5 3703 2188 >>1007_s_at6 2822 1812 >> >>I tried: >> >>GN<-probeNames(Data) >>PM<-pm(Data) >>MM<-mm(Data) >>Cb<-cbind(GN,PM,MM) > > > Try > > Cb <- data.frame(PM, MM, row.names = make.names(GN, unique = TRUE)) > > HTH, > > Jim > > >>But the Cb output doesn't identify probe pare numbers >> >>1007_s_at 649 371 >>1007_s_at 952 1043 >>1007_s_at 1640 2892 >>1007_s_at 3505 4894 >>1007_s_at 3703 2188 >>1007_s_at 2822 1812 >> >>Of cause I could script for those identifiers but is there a simple way to >>reproduce my old output with this altered pm() and mm()? >> >> >>Thank you >> >>Dmitry >> >>_______________________________________________ >>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.