Hi, I have met one problem when I used justRMA() under Linux. Under R GUI, the code can work, but when I use Rscript to call, it can't work. The code is as follows, inputPath="/data1/caozf/CCLE/expression/cel" outputPath="/data1/caozf/CCLE/expression/processed" phenoinfo="/data1/caozf/CCLE/expression/para/CCLE_Expression.Arrays.si f_2010-09-29.txt" prefix="CCLE_Expression_Entrez_2012-03-09" cdfname="hgu133plus2hsentrezgcdf" #input cel files and phenoinfo library("affy") print("normal1") #input cel files sampleInfo<- read.delim(phenoinfo,sep="\t",header=TRUE) sampleNames<- as.character(sampleInfo$CCLE.name) filelist<- paste(as.character(sampleInfo$Array),".CEL",sep="") print("normal2") #RMA normalization eset<- justRMA(filenames=filelist,celfile.path=inputPath,sampleNames=sampleNa mes,cdfname = cdfname) print("normal3") e <- exprs(eset) e<- round(e,3) print("normal4") # output e<- cbind(rownames(e),e) colnames(e)[1]<- "CCLE.Name" write.table(e,paste(outputPath,"/",prefix,"_rma.txt",sep=""),sep="\t", quote=FALSE,row.names=F,append=F, col.names=T) The code file was named PreprocessAffyExp.CCLE.r, and the log are as follows, [caozf@helix para]$ Rscript PreprocessAffyExp.CCLE.r Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. [1] "normal1" [1] "normal2" Execution halted So, we can make sure that, justRMA can not work. But I don't know how to deal with? Any help is appriciate. -- Zongfu Cao *BeiGene(Beijing) Co.,Ltd* No.30 Science Park Road Zhong-Guan-Cun Life Science Park Changping District, Beijing P.R.China Postal Code: 102206 [[alternative HTML version deleted]]

Hi Cao Zongfu, On 3/9/2012 2:15 AM, cao zongfu wrote: > Hi, > I have met one problem when I used justRMA() under Linux. Under R GUI, > the code can work, but when I use Rscript to call, it can't work. The code > is as follows, > > inputPath="/data1/caozf/CCLE/expression/cel" > outputPath="/data1/caozf/CCLE/expression/processed" > phenoinfo="/data1/caozf/CCLE/expression/para/CCLE_Expression.Arrays. sif_2010-09-29.txt" > prefix="CCLE_Expression_Entrez_2012-03-09" > cdfname="hgu133plus2hsentrezgcdf" > > #input cel files and phenoinfo > library("affy") > print("normal1") > #input cel files > sampleInfo<- read.delim(phenoinfo,sep="\t",header=TRUE) > sampleNames<- as.character(sampleInfo$CCLE.name) > filelist<- paste(as.character(sampleInfo$Array),".CEL",sep="") > print("normal2") > > #RMA normalization > eset<- > justRMA(filenames=filelist,celfile.path=inputPath,sampleNames=sample Names,cdfname > = cdfname) > print("normal3") > e<- exprs(eset) > e<- round(e,3) > print("normal4") > > # output > e<- cbind(rownames(e),e) > colnames(e)[1]<- "CCLE.Name" > > write.table(e,paste(outputPath,"/",prefix,"_rma.txt",sep=""),sep="\t ",quote=FALSE,row.names=F,append=F, > col.names=T) > > The code file was named PreprocessAffyExp.CCLE.r, and the log are as > follows, > [caozf at helix para]$ Rscript PreprocessAffyExp.CCLE.r > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'. > > [1] "normal1" > [1] "normal2" > Execution halted > > So, we can make sure that, justRMA can not work. But I don't know how to > deal with? > Any help is appriciate. This isn't due to a problem with justRMA(), it has to do with how underlying methods are being loaded. The explanation is really not useful or important for 99% of end users (and without further investigation, I am not exactly sure what is going on anyway), so I won't get into that here. What you do need to know is that this issue has been corrected in the development version of Bioconductor. So if you want to use Rscript for your pre-processing step, you should upgrade to R-devel (which will be released as R-2.15.0 on 30Mar, so it's not really that developmental at this stage) and BioC-devel. Best, Jim > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099