[BioC] Package "xps" import.data error

Mon Mar 9 21:55:45 CET 2009

Dear Yonghong

First, please reply always to the list, too. This will allow others to 
search the mailing list.

The error message you get means that your CEL-files must be pretty old, 
since they contain in the header part "DatHeader=" of the CEL-files the 
chip type "HuEx-1_0-st-v1.1sq".

The suggestion to change the name of HuEx-1_0-st-v2 to HuEx-1_0-st-v1 is 
one possibility.

Another possibility is to change the header of the CEL-files as 
Affymetrix did, see:
http://www.affymetrix.com/analysis/netaffx/exon/announcements.affx
"changed the chiptype setting in the CEL files from HuEx-1_0-st-v1 to 
HuEx-1_0-st-v2"

The above link also explains why it would be a bad idea to use the 
original HuEx-1_0-st-v1.pgf file for further analysis.

Best regards
Christian

Wang, Yonghong (NIH/NCI) [C] wrote:
>
> Dear Christian:
>
> Thanks for your quick response. According to your suggestions, I 
> reinstalled the newest version of xps package and reran the code under 
> the "RTerm" and got the following error message:
>
> *Opening file 
> <c:/R_file/CRAN/Workspaces/Schemes/Scheme_HuEx10stv2r2_na27f.root> in 
> <READ> mode...*
>
> *Creating new file <c:/R_file/ROOTData/test_data_cel.root>...*
>
> *Importing <c:/R_file/CEL/H2452.CEL> as <H2452.cel>...*
>
> *Error: Selected scheme <HuEx-1_0-st-v2> is not identical to imported 
> scheme <HuEx-1_0-st-v1>.*
>
> *Error: Selected scheme <c:/R_file/CEL/H2452.CEL> is not identical to 
> imported scheme <>.*
>
> *Error in import.data(scheme.exon, "test_data", filedir = datdir, 
> celdir = celdir, :*
>
> * error in function 'ImportData'*
>
> Search Rmailing list, one suggestion is to change the name of 
> HuEx-1_0-st-v2 to HuEx-1_0-st-v1 (since I could not find the cdf of 
> HuEx-1_0-st-v1. In my case, I use the following code to generate the 
> Root.scheme:
>
> *scheme.huex10stv2r2.na27e <- 
> import.exon.scheme("Scheme_HuEx10stv2r2_na27e",filedir=scmdir,*
>
> * layoutfile=paste(libdir,"HuEx-1_0-st-v1.r1.clf",sep="/"),*
>
> * schemefile=paste(libdir,"HuEx-1_0-st-v1.r1.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="/"))*
>
> In which I simply change the name of “HuEx-1_0-st-v2.r2.clf” to 
> “HuEx-1_0-st-v1.r1.clf”, and “HuEx-1_0-st-v2.r2.pgf” to 
> “HuEx-1_0-st-v1.r1.pgf”, without changing the actual content of clf 
> and pfg file. So far it works. My questions (or concerns) are whether 
> these kinds of changes are valid, and whether these changes affect the 
> final annotation result?
>
> Thanks for the help
>
> Best regards
>
> Yonghong
>
> -----Original Message-----
> From: cstrato [mailto:cstrato at aon.at]
> Sent: Monday, March 09, 2009 3:03 PM
> To: Wang, Yonghong (NIH/NCI) [C]
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Package "xps" import.data error
>
> 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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>
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>
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>
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>