[BioC] problems with pdInfoBuilder

[James W. MacDonald]

Hi Rene,

maerker at atlas-biolabs.de wrote:
> 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,
> http://www.ceri.memphis.edu/computer/docs/unix/sed.htm
sed
> René
> 
> 
> Code:
> 
>> 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

This is caused by the fact that the 50K annotation files have different 
column headers and different column order (and different columns) as 
compared to the more recent SNP chips.

The quick fix is to use the devel version of pdInfoBuilder, which can 
handle this fact.

Best,

Jim




> Timing stopped at: 0.017 0 0.017 0 0
> 
> 
> 
>> sessionInfo()
> R version 2.6.1 (2007-11-26)
> x86_64-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=de_LU.UTF-8;LC_NUMERIC=C;LC_TIME=de_LU.UTF-8;LC_COLLATE=de_LU.UTF-8;LC_MONETARY=de_LU.UTF-8;LC_MESSAGES=de_LU.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623