[BioC] "import.expr.scheme" error in Package "xps"

[cstrato]

Dear Lei,

Please have a look at "xps/examples/script4xps.R" how to create schemes 
for whole genome and exon arrays.
Concretely, you must do:

scheme.hugene10stv1.na31 <- 
import.exon.scheme("Scheme_HuGene10stv1r4_na31", filedir = scmdir,
   file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", 
"HuGene-1_0-st-v1.r4.clf"),
   file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", 
"HuGene-1_0-st-v1.r4.pgf"),
   file.path(anndir, "Version10Sep", 
"HuGene-1_0-st-v1.na31.hg19.probeset.csv"),
   file.path(anndir, "Version10Sep", 
"HuGene-1_0-st-v1.na31.hg19.transcript.csv"))

Please note that the CDF-files for whole genome and exon arrays are not 
supported by Affymetrix and thus can NOT be used to create scheme files. 
(There is no need to remove the header in the annotation files.)

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
_._._._._._._._._._._._._._._._._._


On 11/4/10 10:17 PM, L Huang wrote:
> Dear list,
>
> I need to do a batch effect removal on  a few batches of Affymetrix Human Gene 1.0 ST arrays by using Evan Johnson's ComBat script. Since the input file for ComBat requires detection call information, I decide to use dabg.call () in xps package for the calculation (Human Gene 1.0 ST array doesn't have MM probes). I download the following chip definition and annotation files from Affymetrix web site: Unsupported Human Gene 1.0 ST Array CDF Files (zip, 13 MB), HuGene-1_0-st-v1 Probe Sequences, tabular format (21 MB, 2/23/10), HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 31 (10 MB, 9/3/10), unzip them and put them into respective directories. Then I get the "Error in import.expr.scheme..." message when trying to import chip definition and annotation files to a ROOT scheme. I notice an early post about the similar error (https://stat.ethz.ch/pipermail/bioconductor/2008-October/024718.html) and follow the direction to remove the header in
>   annotation file. However the error still exists. Could anyone shed me some light on solving this problem?
>
> Thanks a lot.
>
> Lei
>
>
>
>> library(xps)
>
> Welcome to xps version 1.8.3
> Â Â Â  an R wrapper for XPS - eXpression Profiling System
> Â Â Â  (c) Copyright 2001-2010 by Christian Stratowa
> Â Â Â
>> libdir<- "C:/mypath/Affy/library"
>> anndir<- "C:/mypath/Affy/annotation"
>> scmdir<- "C:/mypath/CRAN/Workspaces/Schemes"
>
>> scheme.hugene.1.0.st<- import.expr.scheme("Scheme_HuGene_1_0_st_v1.na31", filedir=scmdir,
> +Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â  schemefile=paste(libdir, "HuGene-1_0-st-v1.r3.cdf", sep="/"),
> +Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â  probefile=paste(libdir, "HuGene-1_0-st-v1.hg19.probe.tab", sep="/"),
> +Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â  annotfile=paste(anndir, "HuGene-1_0-st-v1.na31.hg19.annot.csv", sep="/"),
> +Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â  verbose=TRUE)
> Error in import.expr.scheme("Scheme_HuGene_1_0_st_v1.na31", filedir = scmdir,  :
>   error in function ‘ImportExprSchemes’
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252Â  LC_CTYPE=English_United States.1252Â Â
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=CÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> [5] LC_TIME=English_United States.1252Â Â Â
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base   Â
>
> other attached packages:
> [1] xps_1.8.3Â Â Â Â Â Â  R2HTML_2.1Â Â Â Â Â  svSocket_0.9-48 svIDE_0.9-49Â Â
>
> loaded via a namespace (and not attached):
> [1] svMisc_0.9-60 tcltk_2.11.1Â  tools_2.11.1Â  XML_3.2-0.1Â
>>
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