Hello, I just tried to get a probe to accession matching the above annotation database. In particular it does not yield any mappings for accessions. (i.e. x <- hugene10sttranscriptclusterACCNUM mapped_probes <- mappedkeys(x) yields an empty mapped_probes list. I'm Running R 3.1.1 on ubuntu. The loaded packages are: [1] oligo_1.28.2 Biostrings_2.32.1 XVector_0.4.0 [4] IRanges_1.22.10 oligoClasses_1.26.0 hugene10sttranscriptcluster.db_8.1.0 [7] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 DBI_0.2-7 [10] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2 Biobase_2.24.0 [13] BiocGenerics_0.10.0 BiocInstaller_1.14.2 and capture.output(hugene10sttranscriptcluster()) yields: [1] "Quality control information for hugene10sttranscriptcluster:" [2] "" [3] "" [4] "This package has the following mappings:" [5] "" [6] "hugene10sttranscriptclusterACCNUM has 0 mapped keys (of 33297 keys)" [7] "hugene10sttranscriptclusterALIAS2PROBE has 60778 mapped keys (of 103510 keys)" [8] "hugene10sttranscriptclusterCHR has 19962 mapped keys (of 33297 keys)" [9] "hugene10sttranscriptclusterCHRLENGTHS has 93 mapped keys (of 93 keys)" [10] "hugene10sttranscriptclusterCHRLOC has 19424 mapped keys (of 33297 keys)" [11] "hugene10sttranscriptclusterCHRLOCEND has 19424 mapped keys (of 33297 keys)" [12] "hugene10sttranscriptclusterENSEMBL has 19416 mapped keys (of 33297 keys)" [13] "hugene10sttranscriptclusterENSEMBL2PROBE has 20590 mapped keys (of 28046 keys)" [14] "hugene10sttranscriptclusterENTREZID has 19962 mapped keys (of 33297 keys)" [15] "hugene10sttranscriptclusterENZYME has 2201 mapped keys (of 33297 keys)" [16] "hugene10sttranscriptclusterENZYME2PROBE has 958 mapped keys (of 975 keys)" [17] "hugene10sttranscriptclusterGENENAME has 19962 mapped keys (of 33297 keys)" [18] "hugene10sttranscriptclusterGO has 17412 mapped keys (of 33297 keys)" [19] "hugene10sttranscriptclusterGO2ALLPROBES has 17930 mapped keys (of 18078 keys)" [20] "hugene10sttranscriptclusterGO2PROBE has 13970 mapped keys (of 14134 keys)" [21] "hugene10sttranscriptclusterMAP has 19832 mapped keys (of 33297 keys)" [22] "hugene10sttranscriptclusterOMIM has 13778 mapped keys (of 33297 keys)" [23] "hugene10sttranscriptclusterPATH has 5768 mapped keys (of 33297 keys)" [24] "hugene10sttranscriptclusterPATH2PROBE has 229 mapped keys (of 229 keys)" [25] "hugene10sttranscriptclusterPFAM has 18146 mapped keys (of 33297 keys)" [26] "hugene10sttranscriptclusterPMID has 19726 mapped keys (of 33297 keys)" [27] "hugene10sttranscriptclusterPMID2PROBE has 396421 mapped keys (of 412133 keys)" [28] "hugene10sttranscriptclusterPROSITE has 18146 mapped keys (of 33297 keys)" [29] "hugene10sttranscriptclusterREFSEQ has 19873 mapped keys (of 33297 keys)" [30] "hugene10sttranscriptclusterSYMBOL has 19962 mapped keys (of 33297 keys)" [31] "hugene10sttranscriptclusterUNIGENE has 19578 mapped keys (of 33297 keys)" [32] "hugene10sttranscriptclusterUNIPROT has 18193 mapped keys (of 33297 keys)" [33] "" [34] "" [35] "Additional Information about this package:" [36] "" [37] "DB schema: HUMANCHIP_DB" [38] "DB schema version: 2.1" [39] "Organism: Homo sapiens" [40] "Date for NCBI data: 2014-Mar13" [41] "Date for GO data: 20140308" [42] "Date for KEGG data: 2011-Mar15" [43] "Date for Golden Path data: 2010-Mar22" [44] "Date for Ensembl data: 2014-Feb26" It seems like something is broken there showing in line 4: [6] "hugene10sttranscriptclusterACCNUM has 0 mapped keys (of 33297 keys)" Any ideas on how to solve this? Or whether this is a bug on my side or on the package side? Kind Regards Thomas -- Universit? du Luxembourg Facult? des Sciences, de la Technologie et de la Communication Campus Limpertsberg, BRB 2.13 162a, avenue de la Fa?encerie L-1511 Luxembourg Email: thomas.pfau at uni.lu

Hi Thomas, I built that package, and as you note, there are no accession numbers. But maybe that is because I misunderstand something, so I am directly including Marc Carlson in this conversation. Since the annotation packages are Gene ID-centric, I create two files, one with probeid->GeneID, and one with probeid->GeneBank/RefSeq ID. I then use the first file as the primary annotation file, and the second as the 'otherSrc' file. If I then run makeDBPackage(), I get this output: baseMapType is eg Prepending Metadata Creating Genes table Appending Probes Found 0 Probe Accessions Appending Gene Info Found 19962 Gene Names Found 19962 Gene Symbols <snip> But if I then reverse the source files, using the second file as the primary annotation file, and the GeneID file as the 'otherSrc' file, I get: baseMapType is gb or gbNRef Prepending Metadata Creating Genes table Appending Probes Found 21941 Probe Accessions Appending Gene Info Found 20195 Gene Names Found 20195 Gene Symbols <snip> >From my understanding of the SQLForge vignette, I should be able to use either ordering, and get identical results, but obviously this is not the case. Marc, can you shed some light on this? Evidently I should re- make the packages using gbNRef rather than eg as the baseMapType. Best, Jim On Fri, Aug 29, 2014 at 4:30 AM, Thomas Pfau <thomas.pfau at="" uni.lu=""> wrote: > Hello, > > I just tried to get a probe to accession matching the above annotation > database. In particular it does not yield any mappings for accessions. (i.e. > x <- hugene10sttranscriptclusterACCNUM > mapped_probes <- mappedkeys(x) > yields an empty mapped_probes list. > > > I'm Running R 3.1.1 on ubuntu. > The loaded packages are: > > [1] oligo_1.28.2 Biostrings_2.32.1 XVector_0.4.0 > [4] IRanges_1.22.10 oligoClasses_1.26.0 hugene10sttranscriptcluster. > db_8.1.0 > [7] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 DBI_0.2-7 > [10] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2 Biobase_2.24.0 > [13] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > and capture.output(hugene10sttranscriptcluster()) yields: > [1] "Quality control information for hugene10sttranscriptcluster:" > [2] "" > [3] "" > [4] "This package has the following mappings:" > [5] "" > [6] "hugene10sttranscriptclusterACCNUM has 0 mapped keys (of 33297 keys)" > [7] "hugene10sttranscriptclusterALIAS2PROBE has 60778 mapped keys (of > 103510 keys)" > [8] "hugene10sttranscriptclusterCHR has 19962 mapped keys (of 33297 > keys)" > [9] "hugene10sttranscriptclusterCHRLENGTHS has 93 mapped keys (of 93 > keys)" > [10] "hugene10sttranscriptclusterCHRLOC has 19424 mapped keys (of 33297 > keys)" > [11] "hugene10sttranscriptclusterCHRLOCEND has 19424 mapped keys (of > 33297 keys)" > [12] "hugene10sttranscriptclusterENSEMBL has 19416 mapped keys (of 33297 > keys)" > [13] "hugene10sttranscriptclusterENSEMBL2PROBE has 20590 mapped keys (of > 28046 keys)" > [14] "hugene10sttranscriptclusterENTREZID has 19962 mapped keys (of 33297 > keys)" > [15] "hugene10sttranscriptclusterENZYME has 2201 mapped keys (of 33297 > keys)" > [16] "hugene10sttranscriptclusterENZYME2PROBE has 958 mapped keys (of 975 > keys)" > [17] "hugene10sttranscriptclusterGENENAME has 19962 mapped keys (of 33297 > keys)" > [18] "hugene10sttranscriptclusterGO has 17412 mapped keys (of 33297 keys)" > [19] "hugene10sttranscriptclusterGO2ALLPROBES has 17930 mapped keys (of > 18078 keys)" > [20] "hugene10sttranscriptclusterGO2PROBE has 13970 mapped keys (of 14134 > keys)" > [21] "hugene10sttranscriptclusterMAP has 19832 mapped keys (of 33297 > keys)" > [22] "hugene10sttranscriptclusterOMIM has 13778 mapped keys (of 33297 > keys)" > [23] "hugene10sttranscriptclusterPATH has 5768 mapped keys (of 33297 > keys)" > [24] "hugene10sttranscriptclusterPATH2PROBE has 229 mapped keys (of 229 > keys)" > [25] "hugene10sttranscriptclusterPFAM has 18146 mapped keys (of 33297 > keys)" > [26] "hugene10sttranscriptclusterPMID has 19726 mapped keys (of 33297 > keys)" > [27] "hugene10sttranscriptclusterPMID2PROBE has 396421 mapped keys (of > 412133 keys)" > [28] "hugene10sttranscriptclusterPROSITE has 18146 mapped keys (of 33297 > keys)" > [29] "hugene10sttranscriptclusterREFSEQ has 19873 mapped keys (of 33297 > keys)" > [30] "hugene10sttranscriptclusterSYMBOL has 19962 mapped keys (of 33297 > keys)" > [31] "hugene10sttranscriptclusterUNIGENE has 19578 mapped keys (of 33297 > keys)" > [32] "hugene10sttranscriptclusterUNIPROT has 18193 mapped keys (of 33297 > keys)" > [33] "" > [34] "" > [35] "Additional Information about this package:" > [36] "" > [37] "DB schema: HUMANCHIP_DB" > [38] "DB schema version: 2.1" > [39] "Organism: Homo sapiens" > [40] "Date for NCBI data: 2014-Mar13" > [41] "Date for GO data: 20140308" > [42] "Date for KEGG data: 2011-Mar15" > [43] "Date for Golden Path data: 2010-Mar22" > [44] "Date for Ensembl data: 2014-Feb26" > > It seems like something is broken there showing in line 4: > [6] "hugene10sttranscriptclusterACCNUM has 0 mapped keys (of 33297 keys)" > > Any ideas on how to solve this? Or whether this is a bug on my side or on > the package side? > > Kind Regards > > Thomas > > > -- > Universit? du Luxembourg > Facult? des Sciences, de la Technologie et de la Communication > Campus Limpertsberg, BRB 2.13 > 162a, avenue de la Fa?encerie > L-1511 Luxembourg > Email: thomas.pfau at uni.lu > > _______________________________________________ > 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 [[alternative HTML version deleted]]