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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
my method is split the values into small pieces and do loop. once it stopped retry it again from the stopped pieces.