Hello ! does anybody failed to convert id using getBM in biomaRt package?
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YinCY ▴ 20
@yincy-17934
Last seen 2.3 years ago
HangZhou, zhejaing

when i do id convertion using getBM() function from biomaRt bioconductor package, from time to time this problem comes up, sometimes decrease the attributes can solve, but sometimes not. is there are any solutions?

> gencode.1 <- getBM(
+     attributes = c("ensembl_gene_id", "ensembl_transcript_id", "entrezgene"),
+     filters = "ensembl_transcript_id",
+     values = gencode$ensembl,
+     mart = mmart
+ )

Batch submitting query [=======>----------------------------------------------------------------------------]  10% eta:  1hError in getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id",  : 
  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 getBM • 282 views
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my method is split the values into small pieces and do loop. once it stopped retry it again from the stopped pieces.

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Mike Smith ★ 5.2k
@mike-smith
Last seen 28 minutes ago
EMBL Heidelberg / de.NBI

It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g.

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "asia")

Values for the mirror argument are: useast, uswest, asia. You'll need to modified the dataset argument if you're not accessing human genes.

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thanks Mike!! this is very helpful and the speed is improved much more.

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