[BioC] error of justRMA() under Linux
James W. MacDonald
jmacdon at uw.edu
Fri Mar 9 17:06:44 CET 2012
Hi Cao Zongfu,
On 3/9/2012 2:15 AM, cao zongfu wrote:
> 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,
> #input cel files and phenoinfo
> #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="")
> #RMA normalization
> = cdfname)
> e<- exprs(eset)
> e<- round(e,3)
> # output
> e<- cbind(rownames(e),e)
> colnames(e)<- "CCLE.Name"
> The code file was named PreprocessAffyExp.CCLE.r, and the log are as
> [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")'.
>  "normal1"
>  "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.
James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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