[BioC] markersymol filter problem

[Siarhei Manakou]

Thanks a lot to everybody who replied! I see that this is a problem for 
now, but it is being dealt with, which is good.

Cheers,
Sergei

Steffen wrote:
> 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
>>
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>>   



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