Hi All, For a while I have been using these lines below to normalize a large Affy data set with customCDFs and gcrma. I can't seem to make it work anymore. For some reason, in the affinity adjustment of gcrma, there is a switch to the affy CDF which gives an error later. Its a bit puzzling. I am confident the cdf name is correct and I even updated the custom CDFs to version 14. I am running R 2.12 and bioconductor 2.7 on a Mac. Can anyone suggest a solution to this? Thanks, Yair #This is my code library(affy) library(gcrma) options(pkgType="source") filenames<-as.character(read.table("../CEL-FileNames3.txt", header=FALSE)[,1 ]) eset <- just.gcrma(filenames, cdfname="hgu133plus2hsentrezg", optimize.by= "memory") data<-as.matrix(exprs(eset)) save(data,file="/tmp/gcrma.normalized.Rbin") This is the error Computing affinitiesLoading required package: AnnotationDbi .Done. Adjusting for optical effect..trying URL ' http://bioconductor.org/packages/2.7/data/annotation/src/contrib/hgu13 3plus2cdf_2.7.0.tar.gz ' Content type 'application/x-gzip' length 4368753 bytes (4.2 Mb) opened URL ================================================== downloaded 4.2 Mb * installing *source* package ‘hgu133plus2cdf’ ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (hgu133plus2cdf) The downloaded packages are in ‘/private/var/folders/hZ/hZWLtN7HGfSpd3FVoI8FFk+++TI/-Tmp-/RtmpfUFkFm/ downloaded_packages’ .......... > source("/Volumes/DataHD/BittnerDataset/RunNormalization.r") Computing affinities.Done. Adjusting for optical effect........................Done. Adjusting for non-specific binding.Error in pms[, i] <- bg.adjust.fullmodel(pms[, i], mm, ncs = NULL, pm.affinities, : number of items to replace is not a multiple of replacement length In addition: Warning messages: 1: In log(mms) - mu.mm : longer object length is not a multiple of shorter object length 2: In mu.pm + rho * (log(mms) - mu.mm) : longer object length is not a multiple of shorter object length 3: In x - bhat : longer object length is not a multiple of shorter object length [[alternative HTML version deleted]]

Hi Yair, On 4/15/2011 10:15 AM, Yair Benita wrote: > Hi All, > > For a while I have been using these lines below to normalize a large Affy > data set with customCDFs and gcrma. I can't seem to make it work anymore. > For some reason, in the affinity adjustment of gcrma, there is a switch to > the affy CDF which gives an error later. Its a bit puzzling. I am confident > the cdf name is correct and I even updated the custom CDFs to version 14. I > am running R 2.12 and bioconductor 2.7 on a Mac. > > Can anyone suggest a solution to this? I'm surprised you ever got it to work. Perhaps this is the first time you used the 'mem' argument? Anyway, thanks for the bug report. Fixed in both release and devel now. These changes should propagate through the system in the next day or so. Look for version 2.24.1 in release. Best, Jim > > Thanks, > > Yair > > > #This is my code > > library(affy) > > library(gcrma) > > options(pkgType="source") > > filenames<-as.character(read.table("../CEL-FileNames3.txt", header=FALSE)[,1 > ]) > > eset<- just.gcrma(filenames, cdfname="hgu133plus2hsentrezg", optimize.by= > "memory") > > data<-as.matrix(exprs(eset)) > > save(data,file="/tmp/gcrma.normalized.Rbin") > > > > This is the error > > > Computing affinitiesLoading required package: AnnotationDbi > > .Done. > > Adjusting for optical effect..trying URL ' > http://bioconductor.org/packages/2.7/data/annotation/src/contrib/hgu 133plus2cdf_2.7.0.tar.gz > ' > > Content type 'application/x-gzip' length 4368753 bytes (4.2 Mb) > > opened URL > > ================================================== > > downloaded 4.2 Mb > > > * installing *source* package ?hgu133plus2cdf? ... > > ** R > > ** data > > ** preparing package for lazy loading > > ** help > > *** installing help indices > > ** building package indices ... > > ** testing if installed package can be loaded > > > * DONE (hgu133plus2cdf) > > > The downloaded packages are in > > ?/private/var/folders/hZ/hZWLtN7HGfSpd3FVoI8FFk+++TI/-Tmp-/RtmpfUFkF m/downloaded_packages? > > .......... > >> source("/Volumes/DataHD/BittnerDataset/RunNormalization.r") > > Computing affinities.Done. > > Adjusting for optical effect........................Done. > > Adjusting for non-specific binding.Error in pms[, i]<- > bg.adjust.fullmodel(pms[, i], mm, ncs = NULL, pm.affinities, : > > number of items to replace is not a multiple of replacement length > > In addition: Warning messages: > > 1: In log(mms) - mu.mm : > > longer object length is not a multiple of shorter object length > > 2: In mu.pm + rho * (log(mms) - mu.mm) : > > longer object length is not a multiple of shorter object length > > 3: In x - bhat : > > longer object length is not a multiple of shorter object length > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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