How to modify an Affybatch object?
3
0
Entering edit mode
Puhong Gao ▴ 140
@puhong-gao-116
Last seen 10.2 years ago
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]]
• 1.0k views
ADD COMMENT
0
Entering edit mode
@rafael-a-irizarry-205
Last seen 10.2 years ago
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 >
ADD COMMENT
0
Entering edit mode
@mai98ftustudservuni-leipzigde-338
Last seen 10.2 years ago
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 >
0
Entering edit mode
Puhong Gao ▴ 140
@puhong-gao-116
Last seen 10.2 years ago
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 > > > >
ADD COMMENT

Login before adding your answer.

Traffic: 736 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6