Hi, I would like to generate affyQCReports for before and after normalization of data. I can obviously generate a QCReport for an affyBatch object quite simply but once I have processed the affyBatch object as follows: eset <- rma(affyBatch) I am unsure about how to get a second QCReport. The rma process would have normalized and background corrected the affyBatch object to create the exprsSet but how can I access this normalized data to create another QCReport? any help would be greatly appreciated. thanks, Sebastien

Hi Sebastien, Running affyQCReport() on an ExpressionSet doesn't really make any sense. Probably 2/3 of the quality metrics are directed towards looking at the raw data (probe-level), and the other 1/3 uses either residuals from fitPLM() or ratios of the expression values. In other words, affyQCReport() already does quality assessment of both pre and post normalized (and summarized) data. Trying to do the probe-level quality metrics on expression values doesn't make sense since you no longer have probe-level data. In addition, rma() doesn't return residuals, so you won't be able to do the boxplot of residuals. Really the only thing you would be able to do would be the RLE() plot, and that is already done by affyQCReport(). Best, Jim Sebastien Gerega wrote: > Hi, > I would like to generate affyQCReports for before and after > normalization of data. I can obviously generate a QCReport for an > affyBatch object quite simply but once I have processed the affyBatch > object as follows: > eset <- rma(affyBatch) > I am unsure about how to get a second QCReport. The rma process would > have normalized and background corrected the affyBatch object to create > the exprsSet but how can I access this normalized data to create another > QCReport? > any help would be greatly appreciated. thanks, > Sebastien > > _______________________________________________ > 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