error using pdInfoBuilder on Affymetrix snp 5.0 array
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Hi Sergii, Sergii Ivakhno wrote: > Hello All, > I experience a problen when trying to build PDInfo Package for an > Affymetrix snp 5.0 array using pdInfoBuilder. > Below are my commands, thanks a lot for your assistance in advance! > Best Wishes, > Sergii > > library("pdInfoBuilder") > cdfFile <- "GenomeWideSNP_5.r2.cdf" > csvAnno <- "GenomeWideSNP_5.na24.annot.csv" > csvSeq <- "GenomeWideSNP_5.probe_tab" > pkg <- new("AffySNPPDInfoPkgSeed", version = "0.1.5",author = "Seth > Falcon", email = "sergii.ivakhno at cancer.org.uk",+ > biocViews = "AnnotationData", genomebuild = "NCBI Build 35, May > 2004",cdfFile = cdfFile, csvAnnoFile = csvAnno,csvSeqFile = csvSeq) > >> makePdInfoPackage(pkg, destDir = ".") > Creating package in ./pd.genomewidesnp.5 > Error in sqliteExecStatement(conn, statement, bind.data, ...) : > RS-DBI driver: (incomplete data binding: expected 7 parameters, > got 0) This is because Affy changed the format of some of the data in the annotation .csv file. Benilton knows about this, and may have already put in the fix in the devel version. However, there are bigger problems than this. If you look at the example in ?AffySNPPDInfoPkgSeed-class, you will see that you need three other input files: spline <- "pd.mapping250k.nsp.spline.params.rda" refd <- "pd.mapping250k.nspRef.rda" crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda" As far as I know these files have not been made for the SNP5.0 chips yet, and I don't think the package build will continue without them. I could be wrong on both counts, so those in the know should speak up if so. Best, Jim > In addition: Warning message: > ignoring zero-row bind.data in: sqliteExecStatement(conn, statement, > bind.data, ...) > Timing stopped at: 8.97 0.25 9.22 NA NA > > > > > > > > sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > pdInfoBuilder oligo BufferedMatrixMethods > BufferedMatrix affyio affxparser > RSQLite DBI Biobase > "1.0.0" "1.0.2-3" "1.0.0" > "1.0.1" "1.4.0" "1.8.3" > "0.5-6" "0.2-4" "1.14.0" > > > > > > > *********************************************** > Sergii Ivakhno, PhD student > Computational Biology Group > Department of Oncology, University of Cambridge > Cancer Research UK Cambridge Research Institute > Li Ka Shing Centre > Robinson Way > Cambridge CB2 0RE > UNITED KINGDOM > Tel: +44 1223 404293 > Fax: +44 1223 404208 > E-mail: Sergii.Ivakhno at cancerresearchuk.org > > https://web.mit.edu/ivakhno/www/ > *********************************************** > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
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On Dec 13, 2007 7:28 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Sergii, > > Sergii Ivakhno wrote: > > Hello All, > > I experience a problen when trying to build PDInfo Package for an > > Affymetrix snp 5.0 array using pdInfoBuilder. > > Below are my commands, thanks a lot for your assistance in advance! > > Best Wishes, > > Sergii > > > > library("pdInfoBuilder") > > cdfFile <- "GenomeWideSNP_5.r2.cdf" > > csvAnno <- "GenomeWideSNP_5.na24.annot.csv" > > csvSeq <- "GenomeWideSNP_5.probe_tab" > > pkg <- new("AffySNPPDInfoPkgSeed", version = "0.1.5",author = "Seth > > Falcon", email = "sergii.ivakhno at cancer.org.uk",+ > > biocViews = "AnnotationData", genomebuild = "NCBI Build 35, May > > 2004",cdfFile = cdfFile, csvAnnoFile = csvAnno,csvSeqFile = csvSeq) > > > >> makePdInfoPackage(pkg, destDir = ".") > > Creating package in ./pd.genomewidesnp.5 > > Error in sqliteExecStatement(conn, statement, bind.data, ...) : > > RS-DBI driver: (incomplete data binding: expected 7 parameters, > > got 0) > > This is because Affy changed the format of some of the data in the > annotation .csv file. Benilton knows about this, and may have already > put in the fix in the devel version. Yes, I asked them to do that because you could not identify what annotation data went with what enzyme (at least for fragment information). Background is the Affymetrix Forum thread 'Fragment-length data in the NetAffx CSV files for GenomeWideSNP_6?' on Sept 19 2007, cf. https://www.affymetrix.com/community/forums/thread.jspa?threadID=4981 &tstart=0 They solved the problem for GenomeWideSNP_6 and used the updated file format for GenomeWideSNP_5. However, the content in the GenomeWideSNP_5 CSV file(s) is broken. See thread 'Fragment-length data in the NetAffx CSV files for GenomeWideSNP_5 (sic)?' on Dec 3 2007 for details: https://www.affymetrix.com/community/forums/thread.jspa?threadID=5341 &tstart=0 There is no response from Affy. In the mean time, in aroma.affymetrix, I use GenomeWideSNP_6 annotation data instead after some validity checks. For details on the problem and the workaround see aroma.affymetrix Page 'GenomeWideSNP_5 - Miscellaneous': http://groups.google.com/group/aroma-affymetrix/web/genomewidesnp-5--- miscellaneous In summary, be careful when using the GenomeWideSNP_5 NetAffx annotation files. /Henrik > > However, there are bigger problems than this. If you look at the example > in ?AffySNPPDInfoPkgSeed-class, you will see that you need three other > input files: > > spline <- "pd.mapping250k.nsp.spline.params.rda" > refd <- "pd.mapping250k.nspRef.rda" > crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda" > > As far as I know these files have not been made for the SNP5.0 chips > yet, and I don't think the package build will continue without them. I > could be wrong on both counts, so those in the know should speak up if so. > > Best, > > Jim > > > > > In addition: Warning message: > > ignoring zero-row bind.data in: sqliteExecStatement(conn, statement, > > bind.data, ...) > > Timing stopped at: 8.97 0.25 9.22 NA NA > > > > > > > > > > > > > > > > sessionInfo() > > R version 2.5.1 (2007-06-27) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > > Kingdom.1252;LC_MONETARY=English_United > > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > > "datasets" "methods" "base" > > > > other attached packages: > > pdInfoBuilder oligo BufferedMatrixMethods > > BufferedMatrix affyio affxparser > > RSQLite DBI Biobase > > "1.0.0" "1.0.2-3" "1.0.0" > > "1.0.1" "1.4.0" "1.8.3" > > "0.5-6" "0.2-4" "1.14.0" > > > > > > > > > > > > > > *********************************************** > > Sergii Ivakhno, PhD student > > Computational Biology Group > > Department of Oncology, University of Cambridge > > Cancer Research UK Cambridge Research Institute > > Li Ka Shing Centre > > Robinson Way > > Cambridge CB2 0RE > > UNITED KINGDOM > > Tel: +44 1223 404293 > > Fax: +44 1223 404208 > > E-mail: Sergii.Ivakhno at cancerresearchuk.org > > > > https://web.mit.edu/ivakhno/www/ > > *********************************************** > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 >
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I'm creating the remaining metadata and fixing the code to accomodate these changes. Soon I'll have something in deve. B On Dec 13, 2007, at 10:28 AM, "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Hi Sergii, > > Sergii Ivakhno wrote: >> Hello All, >> I experience a problen when trying to build PDInfo Package for an >> Affymetrix snp 5.0 array using pdInfoBuilder. >> Below are my commands, thanks a lot for your assistance in advance! >> Best Wishes, >> Sergii >> >> library("pdInfoBuilder") >> cdfFile <- "GenomeWideSNP_5.r2.cdf" >> csvAnno <- "GenomeWideSNP_5.na24.annot.csv" >> csvSeq <- "GenomeWideSNP_5.probe_tab" >> pkg <- new("AffySNPPDInfoPkgSeed", version = "0.1.5",author = "Seth >> Falcon", email = "sergii.ivakhno at cancer.org.uk",+ >> biocViews = "AnnotationData", genomebuild = "NCBI Build 35, May >> 2004",cdfFile = cdfFile, csvAnnoFile = csvAnno,csvSeqFile = csvSeq) >> >>> makePdInfoPackage(pkg, destDir = ".") >> Creating package in ./pd.genomewidesnp.5 >> Error in sqliteExecStatement(conn, statement, bind.data, ...) : >> RS-DBI driver: (incomplete data binding: expected 7 >> parameters, >> got 0) > > This is because Affy changed the format of some of the data in the > annotation .csv file. Benilton knows about this, and may have already > put in the fix in the devel version. > > However, there are bigger problems than this. If you look at the > example > in ?AffySNPPDInfoPkgSeed-class, you will see that you need three other > input files: > > spline <- "pd.mapping250k.nsp.spline.params.rda" > refd <- "pd.mapping250k.nspRef.rda" > crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda" > > As far as I know these files have not been made for the SNP5.0 chips > yet, and I don't think the package build will continue without them. I > could be wrong on both counts, so those in the know should speak up > if so. > > Best, > > Jim > > >> In addition: Warning message: >> ignoring zero-row bind.data in: sqliteExecStatement(conn, statement, >> bind.data, ...) >> Timing stopped at: 8.97 0.25 9.22 NA NA >> >> >> >> >> >> >> >> sessionInfo() >> R version 2.5.1 (2007-06-27) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" >> "datasets" "methods" "base" >> >> other attached packages: >> pdInfoBuilder oligo BufferedMatrixMethods >> BufferedMatrix affyio affxparser >> RSQLite DBI Biobase >> "1.0.0" "1.0.2-3" "1.0.0" >> "1.0.1" "1.4.0" "1.8.3" >> "0.5-6" "0.2-4" "1.14.0" >> >> >> >> >> >> >> *********************************************** >> Sergii Ivakhno, PhD student >> Computational Biology Group >> Department of Oncology, University of Cambridge >> Cancer Research UK Cambridge Research Institute >> Li Ka Shing Centre >> Robinson Way >> Cambridge CB2 0RE >> UNITED KINGDOM >> Tel: +44 1223 404293 >> Fax: +44 1223 404208 >> E-mail: Sergii.Ivakhno at cancerresearchuk.org >> >> https://web.mit.edu/ivakhno/www/ >> *********************************************** >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
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