[BioC] error of justRMA() under Linux

[James W. MacDonald]

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=sampleNames,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