Dear Peder, The first issue you raise is not a problem. You can access components whose names contain spaces simply by quoting the names: RG$other[["G Signal Stdev"]] RG$other[[1]] RG$other$"G Signal Stdev" The second issue, assigning rownames to an RGList object with 'other' columns, is a bug. I've committed a fix to Bioconductor in limma 2.16.5 this morning. You should be able to reinstall the new version of limma in a couple of days. Best wishes Gordon > Date: Wed, 18 Mar 2009 13:48:06 +0100 > From: "Peder Worning" <pwo at="" exiqon.com=""> > Subject: [BioC] Getting additional columns from Imagene files with > read.maimages from limma > To: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > > Hello Bioconductor, > > I am using the read.maimages function from the limma package. But I want > to read two more columns from the Imagene files than default. I have > tried to use the other.columns variable to read the data and it works in > principle, I get the data but not in a format I can use and the "other" > option spoils my naming routine for the spots in the arrays. I'll show > some code and ask how to get around it. In this experiment I have 3 > slides with 14592 spots > > This is how I normally do it and each spot gets its id as the rowname > RG.NQ <- read.maimages(file.NQ, source="imagene", > names=target.NQ$Barcode, > wt.fun=mywtfun(c(1,2,3,4,5,6,7)), > columns=list(f="Signal Mean",b="Background Median")) > > rownames(RG.NQ) <- RG.NQ$genes[,6] > dim(RG.NQ) > [1] 14592 3 > > names(RG.NQ) > [1] "R" "G" "Rb" "Gb" > > [5] "source" "Field.Dimensions" "weights" "printer" > > [9] "genes" > > > > Here follow the new code that gives me troubles > RGp.NQ <- read.maimages(filep.NQ, source="imagene", > names=targetp.NQ$Barcode, > wt.fun=mywtfun(c(1,2,3,4,5,6,7)), > columns=list(f="Signal Mean",b="Background Median"), > other.columns=list(t="Signal Stdev",u="Background Stdev")) > names(RGp.NQ) > [1] "R" "G" "Rb" "Gb" > > [5] "source" "Field.Dimensions" "weights" "other" > > [9] "printer" "genes" > names(RGp.NQ$other) > [1] "G Signal Stdev" "G Background Stdev" "R Signal Stdev" > [4] "R Background Stdev" > > And here starts the problems. How do I read variable names with white > spaces \ or \\ do not work, and how do I recover the original format of > the RGp.NQ object from the list RGp.NQ$other > dim(RGp.NQ) > [1] 14592 3 > 3 slides 14592 spots > > Furthermore I cannot make each spot have its id as rowname > > rownames(RGp.NQ) <- RGp.NQ$genes[,6] > Error in dimnames(object$other[[a]]) <- value : object "object" not > found > > If anyone knows a way around these troubles I'll appreciate it a lot > because I need the Signal Stdev and the Background Stdev to evaluate the > quality of each spot. > > Regards > Peder Worning > > > Best regards > > Exiqon A/S > > Peder Worning, Ph.D. > > Senior Scientist, Biomarker Discovery > > Telephone: +45 45650457 > Telefax: +45 45661888 > E-mail: pwo at exiqon.com > > Bygstubben 3 > DK-2950 Vedbaek > Denmark > www.exiqon.com