Question: problems with pdInfoBuilder
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gravatar for maerker@atlas-biolabs.de
11.6 years ago by
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, Ren? Code: > cdf<-"Mapping50K_Xba240.CDF" > csvAnn<-"Mapping50K_Xba240.na23.annot.csv" > csvSeq<-"Mapping50K_Xba_probe_tab" > pkg <- new("AffySNPPDInfoPkgSeed",version ="0.1.5", author="Ren? M?rker", 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) 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 ----------------------------------------- This email was sent from ATLAS Biolabs GmbH, Koeln/Cologne & Berlin. Sitz der Gesellschaft/Registered Office: Koeln/Cologne, Germany. Registergericht/Commercial Register Koeln/Cologne No HRB 59119, USt- IdNr: DE251633620 Diese E-Mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtuemlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfaeltigung oder Weitergabe der E-Mail ausdruecklich untersagt. Bitte benachrichtigen Sie uns und vernichten Sie die empfangene E-Mail. Vielen Dank. This e-mail may contain trade secrets or privileged, undisclosed, or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying, or distribution of it is strictly prohibited. Please inform us immediately and destroy the original transmittal. Thank you for your cooperation.
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ADD COMMENTlink modified 11.6 years ago by James W. MacDonald51k • written 11.6 years ago by maerker@atlas-biolabs.de10
Answer: problems with pdInfoBuilder
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gravatar for James W. MacDonald
11.6 years ago by
United States
James W. MacDonald51k wrote:
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 > Ren? > > > Code: > >> cdf<-"Mapping50K_Xba240.CDF" >> csvAnn<-"Mapping50K_Xba240.na23.annot.csv" >> csvSeq<-"Mapping50K_Xba_probe_tab" >> pkg <- new("AffySNPPDInfoPkgSeed",version ="0.1.5", author="Ren? > M?rker", 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_U S.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 > > > > > > ----------------------------------------- > This email was sent from ATLAS Biolabs GmbH, Koeln/Cologne & Berlin. > Sitz der Gesellschaft/Registered Office: Koeln/Cologne, Germany. > Registergericht/Commercial Register Koeln/Cologne No HRB 59119, USt- IdNr: DE251633620 > > Diese E-Mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtuemlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfaeltigung oder Weitergabe der E-Mail ausdruecklich untersagt. Bitte benachrichtigen Sie uns und vernichten Sie die empfangene E-Mail. Vielen Dank. > > This e-mail may contain trade secrets or privileged, undisclosed, or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying, or distribution of it is strictly prohibited. Please inform us immediately and destroy the original transmittal. Thank you for your cooperation. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
ADD COMMENTlink written 11.6 years ago by James W. MacDonald51k
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