[BioC] makeTranscriptDbFromBiomart error
Stefanie
stefanie.tauber at univie.ac.at
Wed Jun 6 16:03:24 CEST 2012
Hi,
here is my code:
library(GenomicFeatures)
humanDB = makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"hsapiens_gene_ensembl")
This is the error I get thrown:
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... Fehler in
.extractCdsRangesFromBiomartTable(bm_table) :
BioMart data anomaly: some 5' UTR have a start > end
Seems to be a problem of biomart not of R?
Anybody any idea?
Best,
Stefanie
sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.6.5 AnnotationDbi_1.16.10 Biobase_2.14.0
GenomicRanges_1.6.4 IRanges_1.12.5 biomaRt_2.10.0
loaded via a namespace (and not attached):
[1] Biostrings_2.22.0 BSgenome_1.22.0 DBI_0.2-5 RCurl_1.8-0
RSQLite_0.11.1 rtracklayer_1.14.4 tools_2.14.1 XML_3.6-2
[9] zlibbioc_1.0.0
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