Hi, I am wondering if it is possible to obtain the normalized probe values after quantile normalization. I have tried the option of using the destructive=F and then looked at the intensity matrix and found the values to be unchanged. I would like to know the different between the probe matrix and the intensity matrix. The index/order has been changed in the probe matrix from the intensity matrix and for my case the number of rows is reduced for the probe matrix. I will probably need to do the quantile normalization separate from RMA to get the probe intensity values? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu

Hi Lana, > library(affy) > data(affybatch.example) > tmp <- normalize(affybatch.example) > all.equal(exprs(affybatch.example), exprs(tmp)) [1] "Mean relative difference: 0.1390075" > cbind(pm(affybatch.example, "A28102_at")[,1], pm(tmp, "A28102_at")[,1]) [,1] [,2] A28102_at1 149.0 132.0667 A28102_at2 143.5 127.3167 A28102_at3 132.0 115.8333 A28102_at4 130.0 113.7167 A28102_at5 115.8 100.3667 A28102_at6 131.0 114.4333 A28102_at7 131.8 115.4000 A28102_at8 140.0 123.6667 A28102_at9 122.0 106.3333 A28102_at10 133.3 117.2000 A28102_at11 136.0 120.1000 A28102_at12 123.0 107.3333 A28102_at13 132.5 116.5000 A28102_at14 130.0 113.7167 A28102_at15 125.0 109.0333 A28102_at16 133.5 117.3333 Best, Jim Lana Schaffer wrote: > Hi, > I am wondering if it is possible to obtain the > normalized probe values after quantile normalization. > I have tried the option of using the destructive=F > and then looked at the intensity matrix and found the > values to be unchanged. > I would like to know the different between the probe > matrix and the intensity matrix. The index/order > has been changed in the probe matrix from the intensity > matrix and for my case the number of rows is reduced > for the probe matrix. > I will probably need to do the quantile normalization > separate from RMA to get the probe intensity values? > > Lana Schaffer > Biostatistics/Informatics > The Scripps Research Institute > DNA Array Core Facility > La Jolla, CA 92037 > (858) 784-2263 > (858) 784-2994 > schaffer at scripps.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623