Hello- I'm using the affy spike-in latin square data to try to determine which summarization technique is the best. I was wondering if anyone new what normalization technique mas5 uses in BioConductor. I have been using quantiles for rma, dChip, plier, and gcrma. I just used the mas5() command to normalize and summarize without considering its technique. I have to go back and renormalize and resummarize if quantile normalization is not its default normalization method in order to yield more consistant data. Thank you, Brian Bennett brianb00@gwu.edu

The mas5 algorithm scales the data to have the same mean (500 is the default). This corresponds to what Affy has published in their documentation. You can look at the code by typing affy.scalevalue.exprSet at an R prompt, or look at the man page by prepending that with a ?. HTH, Jim 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 >>> Brian Bennett <brianb00@gwu.edu> 07/14/04 02:26PM >>> Hello- I'm using the affy spike-in latin square data to try to determine which summarization technique is the best. I was wondering if anyone new what normalization technique mas5 uses in BioConductor. I have been using quantiles for rma, dChip, plier, and gcrma. I just used the mas5() command to normalize and summarize without considering its technique. I have to go back and renormalize and resummarize if quantile normalization is not its default normalization method in order to yield more consistant data. Thank you, Brian Bennett brianb00@gwu.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I believe it's also quantile if you use affy package. Frank -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Brian Bennett Sent: Wednesday, July 14, 2004 14:26 To: bioconductor@stat.math.ethz.ch Subject: [BioC] what normalization method does mas5 use Hello- I'm using the affy spike-in latin square data to try to determine which summarization technique is the best. I was wondering if anyone new what normalization technique mas5 uses in BioConductor. I have been using quantiles for rma, dChip, plier, and gcrma. I just used the mas5() command to normalize and summarize without considering its technique. I have to go back and renormalize and resummarize if quantile normalization is not its default normalization method in order to yield more consistant data. Thank you, Brian Bennett brianb00@gwu.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Oh, no, mas5 assigns a scaling factor: default is 500. Frank -----Original Message----- From: F Duan [mailto:f.duan@yale.edu] Sent: Wednesday, July 14, 2004 15:22 To: 'Brian Bennett'; 'bioconductor@stat.math.ethz.ch' Subject: RE: [BioC] what normalization method does mas5 use I believe it's also quantile if you use affy package. Frank -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Brian Bennett Sent: Wednesday, July 14, 2004 14:26 To: bioconductor@stat.math.ethz.ch Subject: [BioC] what normalization method does mas5 use Hello- I'm using the affy spike-in latin square data to try to determine which summarization technique is the best. I was wondering if anyone new what normalization technique mas5 uses in BioConductor. I have been using quantiles for rma, dChip, plier, and gcrma. I just used the mas5() command to normalize and summarize without considering its technique. I have to go back and renormalize and resummarize if quantile normalization is not its default normalization method in order to yield more consistant data. Thank you, Brian Bennett brianb00@gwu.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor