Question: AnnotationDBI
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7.2 years ago by
Guest User12k
Guest User12k wrote:
Hi all, I am contacting you regarding a problem with the AnnotationDBI package. I am trying to generate my own database from Agilent chips (surprise, surprise, problems with these again), and keep running into the same problem. Any advice would be very welcome! I have created an input (test.txt) but it really doesn???t matter how long or weather I select for refseq or genbank entries. Everything seems up to date, and no matter what input, the same error occurs. Don???t hate me, I???ve no choice, but is it because I use windows? test.txt ######################## A_24_P66027 NM_00490 A_23_P212522 NM_01461 A_24_P9671 NM_001539 A_24_P801451 NM_006709 A_32_P30710 NM_000978 ######################## I am calling: ######################## makeDBPackage(???HUMANCHIP_DB???, affy = FALSE, prefix = "test", fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt", baseMapType = "refseq", outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\", version = "1.0.0", manufacturer = "Agilent", chipName = "test", manufacturerUrl = "http://www.agilent.com") ######################## Getting the output: ######################## Loading required package: RSQLite Loading required package: DBI baseMapType is refseq Prepending Metadata Creating Genes table Appending Probes Found 5 Probe Accessions Appending Gene Info Found 3 Gene Names Found 3 Gene Symbols Appending Chromosomes Appending Cytogenetic Locations Appending Omim Appending RefSeq Appending Pubmed Appending Unigene Appending ChrLengths Appending 3 GO tables Appending 3 GO ALL tables Appending KEGG Appending EC Appending Chromosome Locations Appending Pfam Appending Prosite Appending Alias Appending Ensembl Appending Uniprot Appending Metadata simplifying probes table dropping redundant data Error in makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), : subscript out of bounds ######################## ######################## > traceback() 4: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), dest_dir = outputDir) 3: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), dest_dir = outputDir) 2: AnnotationDbi:::.makeHUMANCHIP_DB(...) 1: makeDBPackage(???HUMANCHIP_DB???, affy = FALSE, prefix = "test", fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt", baseMapType = "refseq", outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\", version = "1.0.0", manufacturer = "Agilent", chipName = "test", manufacturerUrl = "http://www.agilent.com") ######################### Many thanks, Nick Burgoyne -- output of sessionInfo(): sessionInfo() R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.11.2 DBI_0.2-5 limma_3.12.3 [4] AnnotationDbi_1.18.3 Biobase_2.16.0 BiocGenerics_0.2.0 [7] BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.
go chipname probe affy • 744 views
ADD COMMENTlink modified 7.2 years ago by James W. MacDonald52k • written 7.2 years ago by Guest User12k
Answer: AnnotationDBI
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7.2 years ago by
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James W. MacDonald52k wrote:
Hi Nick, On 9/26/2012 11:42 AM, Nick Burgoyne [guest] wrote: > Hi all, > > I am contacting you regarding a problem with the AnnotationDBI package. > > I am trying to generate my own database from Agilent chips (surprise, surprise, problems with these again), and keep running into the same problem. > > Any advice would be very welcome! > > I have created an input (test.txt) but it really doesn???t matter how long or weather I select for refseq or genbank entries. > > Everything seems up to date, and no matter what input, the same error occurs. > > Don???t hate me, I???ve no choice, but is it because I use windows? Ugh. These nasty windows people... ;-D > > test.txt > ######################## > A_24_P66027 NM_00490 > A_23_P212522 NM_01461 > A_24_P9671 NM_001539 > A_24_P801451 NM_006709 > A_32_P30710 NM_000978 > ######################## > > I am calling: > ######################## > makeDBPackage(???HUMANCHIP_DB???, > affy = FALSE, > prefix = "test", > fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt", > baseMapType = "refseq", > outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\", Here is a stab in the dark. If you notice below, there is a paste(outputdir, "/", prefix, ".sqlite"), which will result in C:\\Users\\np221\\BioinfWork\\AgilentRDatabases\\/test.sqlite Which might result in a problem. Note that R on windows will happily use forward slashes, so you could change outputDir to C:/Users/nb221/BioinfWork/AgilentRdatabases. I would personally omit the trailing forward slash, but in my experience I haven't seen too much backlash if one is used (and you end up with double forward slashes in your file path). In addition, you need to include an author and maintainer field, and the maintainer field has to be something like "Me <me at="" mine.com="">" or when you try to build/check/install R will fail with a complaint about a misformed field in your DESCRIPTION file. Best, Jim > version = "1.0.0", > manufacturer = "Agilent", > chipName = "test", > manufacturerUrl = "http://www.agilent.com") > ######################## > > Getting the output: > ######################## > Loading required package: RSQLite > Loading required package: DBI > baseMapType is refseq > Prepending Metadata > Creating Genes table > Appending Probes > Found 5 Probe Accessions > Appending Gene Info > Found 3 Gene Names > Found 3 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Uniprot > Appending Metadata > > > simplifying probes table > dropping redundant data > Error in makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), : > subscript out of bounds > ######################## > > ######################## >> traceback() > 4: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), > dest_dir = outputDir) > 3: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), > dest_dir = outputDir) > 2: AnnotationDbi:::.makeHUMANCHIP_DB(...) > 1: makeDBPackage(???HUMANCHIP_DB???, affy = FALSE, prefix = "test", fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt", > baseMapType = "refseq", outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\", > version = "1.0.0", manufacturer = "Agilent", chipName = "test", > manufacturerUrl = "http://www.agilent.com") > ######################### > > Many thanks, > > Nick Burgoyne > > > -- output of sessionInfo(): > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RSQLite_0.11.2 DBI_0.2-5 limma_3.12.3 > [4] AnnotationDbi_1.18.3 Biobase_2.16.0 BiocGenerics_0.2.0 > [7] BiocInstaller_1.4.7 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 stats4_2.15.1 tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 7.2 years ago by James W. MacDonald52k
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