Hi, all, Is it possible to insert the modified PM values back to the original affybatch and then to normalize it? I'd like to use the averaged intensities of my technical replicates to normalize against other biological replicates. Any comments and/or suggestions will be very appreciated. Thank you. Puhong Gao, PhD Dev. Psychobiology NYSPI, Unit# 40 1051 Riverside Dr. New York, NY 10032 (212) 543-5710 [[alternative HTML version deleted]]

you can use the pm method, e.g to put the mean of the pms in the first column (array) use: pm(abatch)[,1] <- rowMeans(pm(abatch)) On Mon, 1 Mar 2004, Puhong Gao wrote: > Hi, all, > > Is it possible to insert the modified PM values back to the original affybatch and then to normalize it? I'd like to use the averaged intensities of my technical replicates to normalize against other biological replicates. Any comments and/or suggestions will be very appreciated. Thank you. > > Puhong Gao, PhD > Dev. Psychobiology > NYSPI, Unit# 40 > 1051 Riverside Dr. > New York, NY 10032 > (212) 543-5710 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Puhong, The function "pm<-" should do the job. Type > help("AffyBatch-class") for more information. Johannes Quoting Puhong Gao <pgao@hunter.cuny.edu>: > Hi, all, > > Is it possible to insert the modified PM values back to the original > affybatch and then to normalize it? I'd like to use the averaged > intensities of my technical replicates to normalize against other > biological replicates. Any comments and/or suggestions will be very > appreciated. Thank you. > > Puhong Gao, PhD > Dev. Psychobiology > NYSPI, Unit# 40 > 1051 Riverside Dr. > New York, NY 10032 > (212) 543-5710 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Got it! Many thanks to Rafael and Johannes for their help. Best, Puhong ----- Original Message ----- From: "Rafael A. Irizarry" <ririzarr@jhsph.edu> To: "Puhong Gao" <pgao@hunter.cuny.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Monday, March 01, 2004 1:28 PM Subject: Re: [BioC] How to modify an Affybatch object? > you can use the pm method, e.g to put the mean of the pms in the first > column (array) use: > > pm(abatch)[,1] <- rowMeans(pm(abatch)) > > On Mon, 1 Mar 2004, Puhong Gao wrote: > > > Hi, all, > > > > Is it possible to insert the modified PM values back to the original affybatch and then to normalize it? I'd like to use the averaged intensities of my technical replicates to normalize against other biological replicates. Any comments and/or suggestions will be very appreciated. Thank you. > > > > Puhong Gao, PhD > > Dev. Psychobiology > > NYSPI, Unit# 40 > > 1051 Riverside Dr. > > New York, NY 10032 > > (212) 543-5710 > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >