Hi, We noticed a problem/change with the affy pm function when going from the Drosophila 1 chips to the Drosophila 2.0 chips. I've figure out an easy solution, so I thought I'd point out the problem and solution. When working with the Dros1 chips, the following commands: > pmraw<- pm(raw) > write.table(pmraw,"pmraw.csv",quote=F,sep=",", col.names=NA) would output a csv file with a column of the gene names with probe number at the end, along with a column for each chip's pm values. However, when the same code is used with the Dros 2.0 chips, instead of the gene names and probe numbers, the first column just has the number of the row (1 to 265,358!). The quick fix I found is to do: > gn<-geneNames(raw) > pmraw<-pm(raw,gn) > write.table(pmraw,file="pmraw.csv",quote=F,sep=",",col.names=NA) I'm not sure why this change occurred - maybe it has something to do with the new binary format of the chips? Would there be any other functions (besides mm obviously) that might have similar problems/changes with the new chips? Thanks, Jenny Jenny Drnevich, Ph.D. Department of Animal Biology University of Illinois 515 Morrill Hall 505 S Goodwin Ave Urbana, IL 61801 USA ph: 217-244-6826 fax: 217-244-4565 e-mail: drnevich@uiuc.edu

are you sure this is not a diffeence between two version of the affy package? in the latest version (1.4.x) we made a change to make the "pm" method faster when you want all the pms back. the drawback is you dont get the rownames as before. if you want the rownames you can use: probes(raw,"pm") or pm(raw,genenames=genaNames(raw)) sorry about any inconvinience this has caused. On Mon, 12 Jul 2004, Jenny Drnevich wrote: > Hi, > > We noticed a problem/change with the affy pm function when going from the > Drosophila 1 chips to the Drosophila 2.0 chips. I've figure out an easy > solution, so I thought I'd point out the problem and solution. When working > with the Dros1 chips, the following commands: > > > pmraw<- pm(raw) > > write.table(pmraw,"pmraw.csv",quote=F,sep=",", col.names=NA) > > would output a csv file with a column of the gene names with probe number > at the end, along with a column for each chip's pm values. However, when > the same code is used with the Dros 2.0 chips, instead of the gene names > and probe numbers, the first column just has the number of the row (1 to > 265,358!). The quick fix I found is to do: > > > gn<-geneNames(raw) > > pmraw<-pm(raw,gn) > > write.table(pmraw,file="pmraw.csv",quote=F,sep=",",col.names=NA) > > I'm not sure why this change occurred - maybe it has something to do with > the new binary format of the chips? Would there be any other functions > (besides mm obviously) that might have similar problems/changes with the > new chips? > > Thanks, > Jenny > > > > Jenny Drnevich, Ph.D. > Department of Animal Biology > University of Illinois > 515 Morrill Hall > 505 S Goodwin Ave > Urbana, IL 61801 > USA > > ph: 217-244-6826 > fax: 217-244-4565 > e-mail: drnevich@uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

You're right - I also changed versions of Bioconductor as well as Dros chips. Your second solution is the same as mine, except in one line. I did notice that "pm" works much faster now! Thanks, Jenny At 02:16 PM 7/12/2004 -0400, Rafael A. Irizarry wrote: >are you sure this is not a diffeence between two version of the affy >package? > >in the latest version (1.4.x) we made a change to make the "pm" >method faster when you want all the pms back. >the drawback is you dont get the >rownames as before. if you want the rownames you can use: > >probes(raw,"pm") >or >pm(raw,genenames=genaNames(raw)) > >sorry about any inconvinience this has caused. > > >On Mon, 12 Jul 2004, Jenny Drnevich wrote: > > > Hi, > > > > We noticed a problem/change with the affy pm function when going from the > > Drosophila 1 chips to the Drosophila 2.0 chips. I've figure out an easy > > solution, so I thought I'd point out the problem and solution. When > working > > with the Dros1 chips, the following commands: > > > > > pmraw<- pm(raw) > > > write.table(pmraw,"pmraw.csv",quote=F,sep=",", col.names=NA) > > > > would output a csv file with a column of the gene names with probe number > > at the end, along with a column for each chip's pm values. However, when > > the same code is used with the Dros 2.0 chips, instead of the gene names > > and probe numbers, the first column just has the number of the row (1 to > > 265,358!). The quick fix I found is to do: > > > > > gn<-geneNames(raw) > > > pmraw<-pm(raw,gn) > > > write.table(pmraw,file="pmraw.csv",quote=F,sep=",",col.names=NA) > > > > I'm not sure why this change occurred - maybe it has something to do with > > the new binary format of the chips? Would there be any other functions > > (besides mm obviously) that might have similar problems/changes with the > > new chips? > > > > Thanks, > > Jenny > > > > > > > > Jenny Drnevich, Ph.D. > > Department of Animal Biology > > University of Illinois > > 515 Morrill Hall > > 505 S Goodwin Ave > > Urbana, IL 61801 > > USA > > > > ph: 217-244-6826 > > fax: 217-244-4565 > > e-mail: drnevich@uiuc.edu > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jenny Drnevich, Ph.D. Department of Animal Biology University of Illinois 515 Morrill Hall 505 S Goodwin Ave Urbana, IL 61801 USA ph: 217-244-6826 fax: 217-244-4565 e-mail: drnevich@uiuc.edu