[BioC] markersymol filter problem

[Steffen]

Hi Sergei,

The Ensembl team has been contacted about the loss of markersymbol as 
filter and attribute in the latest release of the Ensembl BioMart.
It looks like this was not intended and they will put the markersymbol 
attribute/filter back. They are planning to put them in next Wednesday 
and then the Ensembl webteam will have to propagate this fix across the 
machines.

We'll have to use Marc's workaround in the meantime.

Cheers,
Steffen

Marc Carlson wrote:
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>