[BioC] markersymol filter problem

[Marc Carlson]

Siarhei Manakou wrote:
> Hello,
>
> I am accessing biomarts through bioconductor. It used to be possible to 
> use list of gene symbols and retrieve pretty much what you wanted using 
> getBM() function and specifying "markersymbol" as filters. Now this 
> thing doesn't work anymore. I know that in order to retrieve gene 
> symbols from, let's say, ensembl geneIDs - you can specify 
> "external_gene_id", as attributes and you will get your list of gene 
> symbols. However things don't work other way around and putting 
> "external_gene_id" as filters doesn't work. So do you know how it is 
> possible to use gene symbols these days in order to retrieve information 
> from biomarts?
>
> thanks,
> Sergei
>
>
>   
It occurs to me that you might be able to use the latest bioconductor
annotation packages to work around this.  You could use an organism
based package to map from gene symbols over to entrez gene IDs for
instance.  Then you could just feed those IDs into biomart instead as a
work around.

So something like:

library("org.Hs.eg.db")
foo <- c("GLP-1","HOTAIR","SCARNA27")
mget(foo,envir=org.Hs.egSYMBOL2EG)


    Marc