I have one problem for the RMA! I got three datasets using different RMA way in R: from the .CEL files, 1, justRMA() d <- ReadAffy() 2, expresso(d, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") 3, bgd <- bg.correct(d,method="rma") probes <- pm(bgd) expression <- generateExprVal.method.medianpolish(probes)$exprs data <- normalize.quantiles(expression) As the results, I got three datasets. I was thinking that these three datasets should be identical because they were obtained from the same procedures! But, the first and second gene expression data are identical, the third gene expression data are different with the other two. Why the third data expression is different? How I can progress and get the data the same as the first two datasets! Thanks a lot, and I am looking forward to hearing the solution soon! regards, meiyin

normalization comes before summarization (median polish). b On Sep 5, 2007, at 10:14 AM, Meiyin.Gao at unibas.ch wrote: > > I have one problem for the RMA! > > I got three datasets using different RMA way in R: > > from the .CEL files, > > 1, justRMA() > > d <- ReadAffy() > 2, expresso(d, bgcorrect.method="rma", normalize.method="quantiles", > pmcorrect.method="pmonly", > summary.method="medianpolish") > 3, > > bgd <- bg.correct(d,method="rma") > probes <- pm(bgd) > expression <- generateExprVal.method.medianpolish(probes)$exprs > data <- normalize.quantiles(expression) > > As the results, I got three datasets. I was thinking that these > three datasets > should be identical because they were obtained from the same > procedures! > > But, the first and second gene expression data are identical, the > third gene > expression data are different with the other two. > > Why the third data expression is different? How I can progress and > get the data > the same as the first two datasets! > > Thanks a lot, and I am looking forward to hearing the solution soon! > regards, > meiyin > > _______________________________________________ > 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

Meiyin.Gao at unibas.ch wrote: > I have one problem for the RMA! > > I got three datasets using different RMA way in R: > > from the .CEL files, > > 1, justRMA() > > d <- ReadAffy() > 2, expresso(d, bgcorrect.method="rma", normalize.method="quantiles", > pmcorrect.method="pmonly", summary.method="medianpolish") > 3, > > bgd <- bg.correct(d,method="rma") > probes <- pm(bgd) > expression <- generateExprVal.method.medianpolish(probes)$exprs > data <- normalize.quantiles(expression) > > As the results, I got three datasets. I was thinking that these three datasets > should be identical because they were obtained from the same procedures! > > But, the first and second gene expression data are identical, the third gene > expression data are different with the other two. In the first two cases you are doing a quantile normalization first (using the PM data). In the third case you are normalizing after the median polish step. Best, Jim > > Why the third data expression is different? How I can progress and get the data > the same as the first two datasets! > > Thanks a lot, and I am looking forward to hearing the solution soon! > regards, > meiyin > > _______________________________________________ > 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 University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623