I use Imagene 4.0 and Limma R package. My source file are into R directory ... and this is my R shell: > library(limma) > YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t", as.is= TRUE) > YourSample SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 1.txt 2.txt treated untreated 2 2 3.txt 4.txt treated untreated 3 3 5.txt 6.txt treated untreated > RG<-read.maimages(slides, source="imagene") Error in match.arg(source, c("spot", "spot.close.open", "genepix", "quantarray")) : ARG should be one of spot, spot.close.open, genepix, quantarray What is the problem? Thanks

Your error message describes the problem. You can choose one of the following for your source: spot, spot.close.open, genepix, or quantarray. You chose imagene, which is not in that list, hence the error. I would imagine that you are using an outdated version of limma that doesn't support the imagene format. You should upgrade to the devel version, which does. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "cv.vc" <cv.vc@libero.it> 10/27/03 07:37AM >>> I use Imagene 4.0 and Limma R package. My source file are into R directory ... and this is my R shell: > library(limma) > YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t", as.is= TRUE) > YourSample SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 1.txt 2.txt treated untreated 2 2 3.txt 4.txt treated untreated 3 3 5.txt 6.txt treated untreated > RG<-read.maimages(slides, source="imagene") Error in match.arg(source, c("spot", "spot.close.open", "genepix", "quantarray")) : ARG should be one of spot, spot.close.open, genepix, quantarray What is the problem? Thanks _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Ciao anonymoso, which version of limma are you using? Is it an up-to-date one that knows about imagene? Best regards Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Mon, 27 Oct 2003, cv.vc wrote: > I use Imagene 4.0 and Limma R package. > My source file are into R directory ... and this is my R shell: > > > library(limma) > > > YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t ",as.is= > TRUE) > > YourSample > SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 > 1 1 1.txt 2.txt treated untreated > 2 2 3.txt 4.txt treated untreated > 3 3 5.txt 6.txt treated untreated > > RG<-read.maimages(slides, source="imagene") > Error in match.arg(source, c("spot", "spot.close.open", "genepix", > "quantarray")) : > ARG should be one of spot, spot.close.open, genepix, quantarray > > What is the problem? Thanks >

Hi, Your steps are: library(limma) > YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t", as.is= TRUE) > slides<-cbind(YourSample$FileNameCy3, YourSample$FileNameCy5) > RG<-read.maimages(slides, source="imagene") . . . Marcelo > > library(limma) > > > > > YourSample > SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 > 1 1 1.txt 2.txt treated untreated > 2 2 3.txt 4.txt treated untreated > 3 3 5.txt 6.txt treated untreated > > RG<-read.maimages(slides, source="imagene") > Error in match.arg(source, c("spot", "spot.close.open", "genepix", > "quantarray")) : > ARG should be one of spot, spot.close.open, genepix, quantarray > > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.532 / Virus Database: 326 - Release Date: 27/10/2003 > ---