Error in biomaRt
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@angelicalindlof-20481
Last seen 2.5 years ago

Error in getBM(attributes = c("ensemblgeneid", "entrezgene", "hgnc_symbol"), : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

I have previously used BioMart without any problems. But now I get this error message, with code that previously worked fine.

My code:

library( "biomaRt" ) res <- fc$counts tmp <- sapply( strsplit( rownames(res), split="\+" ), "[", 1 ) tmp <- sapply( strsplit(tmp, split="\." ), "[", 1 ) res$ensembl <- tmp ensembl = useMart( "ensembl", dataset = "hsapiensgeneensembl" ) genemap <- getBM( attributes = c("ensemblgeneid", "entrezgene", "hgncsymbol"), filters = "ensemblgene_id", values = res$ensembl, mart = ensembl )

fc$counts are gene IDs and counts from featureCounts function.

biomaRt getBM • 322 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 4 hours ago
EMBL Heidelberg / de.NBI

I'm seeing a few reports of this error at the moment, which suggests to me that maybe Ensembl is being quite slow and timing out on your query. Can you try using a different mirror that may be faster? You can do this by running this line before calling getBM():

ensembl = useEnsembl( "ensembl", 
                      dataset = "hsapiens_gene_ensembl", 
                      mirror = "useast" )

Available options for the mirror argument are: 'uswest', 'useast', 'asia'

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Thank you! It seems correct. Now it's working fine and much faster as well. I also tried BiomaRt web server at Ensembl, but that doesn't respond very well either at the moment.

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