biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
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ksomi47 • 0
@ksomi47-22807
Last seen 20 months ago

Hi, I've been tried to make a TxDb object using a function 'makeTxDbFromBiomart' in r package 'GenomicFeatures' but failed. I've got a message to report the error on the webpage. Could you give me what happens while I run this and how will the problem be solved?

Here is the message that I've got:

txdb = makeTxDbFromBiomart(dataset = "mmusculusgeneensembl") Download and preprocess the 'transcripts' data frame ... Error in getBM(attributes, filters = bmfilters, values = bmvalues, ...) : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org

biomart txdb makeTxDbFromBiomart GenomicFeatures • 191 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 6 hours ago
EMBL Heidelberg / de.NBI

The BioMart server seem to be being unreliable at the moment. Could you use the makeTxDbFromEnsembl() function instead? It should use the same data to create the TxDb object.

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@james-w-macdonald-5106
Last seen 6 hours ago
United States

An arguably better idea is to use an already existing 'EnsDb` which should contain pretty much the same content, and doesn't require you to duplicate already expended effort.

> library(AnnotationHub)

> hub <- AnnotationHub()
  |======================================================================| 100%

snapshotDate(): 2019-10-29
> z <- query(hub, c("musculus","ensdb"))
> z
AnnotationHub with 12 records
# snapshotDate(): 2019-10-29 
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53222"]]' 

            title                            
  AH53222 | Ensembl 87 EnsDb for Mus Musculus
  AH53726 | Ensembl 88 EnsDb for Mus Musculus
  AH56691 | Ensembl 89 EnsDb for Mus Musculus
  AH57770 | Ensembl 90 EnsDb for Mus Musculus
  AH60788 | Ensembl 91 EnsDb for Mus Musculus
  ...       ...                              
  AH64944 | Ensembl 94 EnsDb for Mus musculus
  AH67971 | Ensembl 95 EnsDb for Mus musculus
  AH69210 | Ensembl 96 EnsDb for Mus musculus
  AH73905 | Ensembl 97 EnsDb for Mus musculus
  AH75036 | Ensembl 98 EnsDb for Mus musculus

## and if you are dead set on a TxDb with Ensembl IDs
> zz <- query(hub, c("musculus","txdb"))
> zz
AnnotationHub with 6 records
# snapshotDate(): 2019-10-29 
# $dataprovider: UCSC
# $species: Mus musculus
# $rdataclass: TxDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH52263"]]' 

            title                                    
  AH52263 | TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite  
  AH52264 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
  AH52265 | TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite 
  AH66175 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
  AH70594 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
  AH75762 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite

## you could use the TxDb based on the ensGene table from UCSC

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