Hi, I'm performing Affymetrix GeneChip microarray analysis. I I was wondering if the normalization procedure that exploits the hybridization spike intensities is already implemented in one of the Bioconductor packages. If yes, can you kindly indicate me where? I have tried to figure out that by myself looking at the many package guides but it seems it is no part of the current releases. Many Thanks for your time, Federico Comoglio

Hi Federico, On 3/2/2011 12:28 PM, federico.comoglio wrote: > Hi, > > I'm performing Affymetrix GeneChip microarray analysis. I I was > wondering if the normalization procedure that exploits the > hybridization spike intensities is already implemented in one of the > Bioconductor packages. If yes, can you kindly indicate me where? I > have tried to figure out that by myself looking at the many package > guides but it seems it is no part of the current releases. It hasn't been implemented in the affy package, but the functionality exists to add your own normalization methods. See ?upDate.normalize.AffyBatch.methods and the custom processing methods vignette. Best, Jim > > Many Thanks for your time, > > Federico Comoglio _______________________________________________ > Bioconductor mailing list Bioconductor at r-project.org > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues