[BioC] Package "xps" import.data error

[cstrato]

cstrato wrote:
> Dear Yonghong
>
> Since you are using xps with Windows I suppose that you are using RGui.
>
> In order to get more information about your problem may I suggest to 
> run xps using RTerm with verbose=TRUE. This will show you more 
> information and give you a hint about the concrete problem, see:
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025452.html 
>
>
> Could you please send me the complete output from RTerm.
>
> Could you also please update to a newer version of xps, xps_1.0.2 is 
> pretty old.
>
> Maybe, one last note: From your code I assume that you have imported 
> the exon scheme in the same R session as the CEL-files. Since the pgf 
> and annotation files consume huge amounts of memory it is better to 
> import the exon scheme in a separate R session first. When starting a 
> new R session you can use "root.scheme()" to import the created scheme 
> and import the CEL-files in the new R session.
>
> Please let me know if this could solve your problem, otherwise please 
> send me the output from RTerm, as already mentioned.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
>
>
>
> Wang, Yonghong (NIH/NCI) [C] wrote:
>> Hello all:
>>
>> I am new to XPS package and would like to use it to perform affymetrix
>> EXON array data analysis. Basically I copied and paseted the sample
>> codes and ran the analysis. Originally, I tried some test dataset (cel
>> files) and works fine. But when I ran my cel files, I got the error
>> message. Basically I can't import the Cel files into R package. The code
>> I was using is listed below. I am using window system with R version
>> 2.8.1. I am thinking that the error might be caused by some kinds of
>> incompatibilities, but can't prove it. Any helps would be very
>> appreciated.
>>
>> Best
>>
>> Yonghong
>>
>>  
>>
>> Code:
>>
>>  
>>
>>  
>>> setwd("c:/R_file")
>>>     
>>
>>  
>>> library(xps)
>>>     
>>
>>  
>>
>> Welcome to xps version 1.0.2
>>     an R wrapper for XPS - eXpression Profiling System
>>
>>     (c) Copyright 2001-2008 by Christian Stratowa
>>
>>    
>>  
>>> homedir <- "c:/R_file/"
>>>     
>>
>>  
>>> libdir <- paste(homedir, "libraryfiles", sep="")
>>>     
>>
>>  
>>> anndir <- paste(homedir, "Annotation", sep="")
>>>     
>>
>>  
>>> scmdir <- paste(homedir, "CRAN/Workspaces/Schemes", sep="")
>>>     
>>
>>  
>>> celdir <- paste(homedir, "CEL", sep="")
>>>     
>>
>>  
>>> datdir <- paste(homedir, "ROOTData", sep="")
>>>     
>>
>>  
>>> tmpdir <- paste(homedir, "CRAN/Workspaces/Exon/temp", sep="")
>>>     
>>
>>  
>>> celfiles <- c("H2452.CEL", "H2596.CEL")
>>>     
>>
>>  
>>> celnames <- substring(celfiles,1)
>>>     
>>
>>  
>>> scheme.huex10stv2r2.na27f <-
>>>     
>> import.exon.scheme("Scheme_HuEx10stv2r2_na27f",filedir=scmdir,
>>
>> +
>> layoutfile=paste(libdir,"HuEx-1_0-st-v2.r2.clf",sep="/"),
>>
>> +
>> schemefile=paste(libdir,"HuEx-1_0-st-v2.r2.pgf",sep="/"),
>>
>> +
>> probeset=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.probeset.csv",sep="/"),
>>
>> +
>> transcript=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.transcript.csv",sep="/
>> "))
>>
>>  
>>> scheme.exon
>>>     
>> <-root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na27f.root",sep="/"))
>>
>>  
>>> test.data<- import.data(scheme.exon, "test_data",filedir = datdir,
>>>     
>> celdir = celdir, celfiles = celfiles, verbose = FALSE)
>>
>> Error in import.data(scheme.exon, "test_data", filedir = datdir, celdir
>> = celdir,  :
>>   error in function 'ImportData'
>>
>>  
>>
>>     [[alternative HTML version deleted]]
>>
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>>
>
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