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Wang, Yonghong (NIH/NCI) wrote: > >i.pm <- indexProbes(data, "pm"); > > >>xy.pm <- indices2xyi.pm, abatch = data); > > >>seq.pm <- u133x3pprobe$RESIDUES[xy.pm[,1] == u133x3pprobe$POSITIONX +1)& > > xy.pl[,2] == u133x3pprobe$POSITIONY + 1)]; i.pm <- unlist(indexProbes(data, "pm")) ## note here that 'data' is a poor choice for a variable name ## you are masking an existing function. dat or Data would be better ## convert X and Y values to indices i.pt <- xy2i(u133x3pprobe$x, u133x3pprobe$y) ## match the affybatch order to the probe table order index <- matchi.pm, i.pt) ## extract sequence seqnc <- u133x3pprobe$sequence[index] write.table(cbind(probeNames(data),pm(data),mm(data), seqnc),file="mytest.dat",sep = "\t") HTH, Jim > > > > Y. Wang > > ATC/NCI/NIH > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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

Wang, Yonghong (NIH/NCI) wrote: > Jim: Thanks for the help. It works, and I really love the result. Another > question related to the original one is about the pm value. I am wondering > whether the pm value generated using function pm() are already background > subtracted (same as the method "mas"). If not, how can I subtract the noise > level background (not MM background) of each spot from affy chip? Thanks a > lot for the help. The PM values you are extracting are not background corrected. You can see the available methods for background correction by typing bgcorrect.methods at an R prompt (after loading the affy package). > bgcorrect.methods [1] "mas" "none" "rma" "rma2" If you want the background corrected values: abatch <- bg.correct(abatch, "rma") Where abatch is the name of your affybatch (which I am sure is no longer 'data' ;-D). Then run the rest of the code as before. > By the way, I really like the bioconductor mailing list and have joined > after I submitted my first question a few days ago. I am not quit sure > whether I should also submit this follow-up question to the mailing list. > But I will do so next time. Yes. All followup questions should also go to the list, so others can use the list as a reference for questions that may have already been answered. Best, Jim > > Thanks > Yonghong > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Thursday, June 16, 2005 3:15 PM > To: Wang, Yonghong (NIH/NCI) > Cc: 'bioconductor at stat.math.ethz.ch' > Subject: Re: [BioC] combine pm and oligo sequence information > > Wang, Yonghong (NIH/NCI) wrote: > >> >i.pm <- indexProbes(data, "pm"); >> >> >> >>>xy.pm <- indices2xyi.pm, abatch = data); >> >> >>>seq.pm <- u133x3pprobe$RESIDUES[xy.pm[,1] == u133x3pprobe$POSITIONX +1)& >> >>xy.pl[,2] == u133x3pprobe$POSITIONY + 1)]; > > > > i.pm <- unlist(indexProbes(data, "pm")) > ## note here that 'data' is a poor choice for a variable name > ## you are masking an existing function. dat or Data would be better > > ## convert X and Y values to indices > i.pt <- xy2i(u133x3pprobe$x, u133x3pprobe$y) > ## match the affybatch order to the probe table order > index <- matchi.pm, i.pt) > ## extract sequence > seqnc <- u133x3pprobe$sequence[index] > write.table(cbind(probeNames(data),pm(data),mm(data), > seqnc),file="mytest.dat",sep = "\t") > > HTH, > > Jim > > > >> >> >>Y. Wang >> >>ATC/NCI/NIH >> >> >> >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- 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