[BioC] problems with pdInfoBuilder

maerker at atlas-biolabs.de maerker at atlas-biolabs.de
Tue Mar 4 17:05:04 CET 2008

Hello All,

I get an Error when trying to build PDInfo Package for an
Affymetrix Mapping50k Xba240 array using pdInfoBuilder.
Below are my commands, thanks a lot for your assistance in advance!

Kind Regards,



> cdf<-"Mapping50K_Xba240.CDF"
> csvAnn<-"Mapping50K_Xba240.na23.annot.csv"
> csvSeq<-"Mapping50K_Xba_probe_tab"
> pkg <- new("AffySNPPDInfoPkgSeed",version ="0.1.5", author="René
Märker", email= maerker at atlas-biolabs.de",biocViews="AnnotationData",
genomebuild="NCBI Build 36.1, March 2006",cdfFile= cdf,
csvAnnoFile=csvAnno, csvSeqFile = csvSeq)
> makePdInfoPackage(pkg,destDir = ".")

Creating package in ./pd.mapping50k.xba240

loadUnitsByBatch took 128.72 sec
Fehler in strsplit(v, " // ") : Nicht-Charakter Argument
Timing stopped at: 0.017 0 0.017 0 0

> sessionInfo()
R version 2.6.1 (2007-11-26)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] pdInfoBuilder_1.2.0  oligo_1.2.2          oligoClasses_1.0.3
[4] AnnotationDbi_1.0.6  preprocessCore_1.0.0 affxparser_1.10.2
[7] RSQLite_0.6-7        DBI_0.2-4            Biobase_1.16.3

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

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