[BioC] how to retrieve data in list using getBM in biomaRt package?

[Steffen Durinck]

Hi Shiliang,

It looks like you forgot to specify the output argument as a list.
Try:

genelistM <- getBM(attributes = c("entrezgene","go","uniprot_swissprot_accession", "refseq_dna"), filters =
"entrezgene",values = ll, mart = mart, na.value ="&nbsp;", output="list")

best,
Steffen

swang wrote:
> Hi,Dr. Durinck:
>
>
> I do need to get a list back from getBM function in biomaRt package, I read
> your feedback about getBM when the probe is long.
> http://article.gmane.org/gmane.science.biology.informatics.conductor/9172/match=biomart+rmysql+mode
> but can you tell me how to get a list back using bomaRt RMySQL mode?
> I have a 250 length entrezgene id and try to get back
> genelistM <- getBM(attributes =
> c("entrezgene","go","uniprot_swissprot_accession", "refseq_dna"), filters =
> "entrezgene",
> values = ll, mart = mart, na.value =
> "&nbsp;")
>
> length(ll)
> 250
> ll <- getLL(probe,data = "Rosetta")
>
> I cannot get back in list, otherwise it will tell me wrong.
>
> Thanks
>
> Shiliang
>
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