[BioC] hugene10sttranscriptclusterACCNUM has no mappings
Thomas Pfau
thomas.pfau at uni.lu
Fri Aug 29 10:30:37 CEST 2014
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
--
Université du Luxembourg
Faculté des Sciences, de la Technologie et de la Communication
Campus Limpertsberg, BRB 2.13
162a, avenue de la Faïencerie
L-1511 Luxembourg
Email: thomas.pfau at uni.lu
More information about the Bioconductor
mailing list