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 >

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