[BioC] Help using biomaRt

[James W. MacDonald]

Looking back over this thread, it appears you got a lot of responses, 
for which you graciously thanked the responders. The only question I see 
that wasn't answered was at the end of an extremely long post in which 
you seemed to want to show your thinking when using biomaRt.

I think this was the problem. Most people don't have the time to read 
all that, and probably don't care to know what worked for you. A short 
message showing what you tried and the unexpected result would suffice. 
As would reading the error message and trying to think what it might mean.

You got

Error in getBM(attnames, filters = filtnames, values = affyids, mart = 
mart) :
   Query ERROR: caught BioMart::Exception::Usage: Attributes from 
multiple attribute pages are not allowed

after adding one new attribute. I don't know what this means, really, 
but it would appear that you can't mix ensembl_exon_id with the other 
attributes.

 > results3<-getBM("ensembl_exon_id", filters=filtnames, values=affyids, 
mart=mart)
 > results3
       ensembl_exon_id
1  ENSMUSE00000614004
2  ENSMUSE00000704983
3  ENSMUSE00000641393
4  ENSMUSE00000617038
5  ENSMUSE00000617037
6  ENSMUSE00000617036
7  ENSMUSE00000560065
[snip]

I understand your frustration with biomaRt. When I first started using 
it, I was frustrated as well. It's pretty complicated, but quite 
powerful as well. As with all software there is a learning curve, and 
there is no substitute for experience, and that only comes from trial 
and error.

Best,

Jim




john seers (IFR) wrote:
> 
> Hi Jim
> 
> The empirical evidence would suggest otherwise. :)
> 
> Sigh. Perhaps I'll try submitting my question again sometime soon. Or
> perhaps biomaRt will become clearer if I use it more.
> 
> Regards
> 
> John
> 
> 
> 
>  
> ---
> 
> -----Original Message-----
> From: James MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 23 January 2009 17:14
> To: john seers (IFR)
> Subject: Re: [BioC] Help using biomaRt
> 
> Hi John,
> 
> If you expect any real help you will need to supply us with the code you
> have tried (especially a toy example that people can try themselves) and
> the exact output from R. Also, the output of sessionInfo().
> 
> Best,
> 
> Jim
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646
734-936-8662