Hi Juliet,

The third attribute you're looking for is 'description':

 idens <- getBM(attributes =
c("affy_hg_u133a","hgnc_symbol","description"), filters
="affy_hg_u133a",values = probeSets, mart = ensembl)

Gives:

  affy_hg_u133a hgnc_symbol
                                    description
1     219666_at      MS4A6A              membrane-spanning 4-domains,
subfamily A, member 6A [Source:HGNC Symbol;Acc:13375]
2   220547_s_at      FAM35B                     family with sequence
similarity 35, member B [Source:HGNC Symbol;Acc:31425]
3     218034_at        FIS1 fission 1 (mitochondrial outer membrane)
homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21689]
4   220547_s_at     FAM35B2       family with sequence similarity 35,
member B2 (pseudogene) [Source:HGNC Symbol;Acc:34038]
5   220547_s_at      FAM35A                     family with sequence
similarity 35, member A [Source:HGNC Symbol;Acc:28773]


There is no systematic way to figure out with attribute name you need to
use all you have is the attribute name and a description of the attribute.
 The more you get used to looking at those, the easier it gets to figure
out which one you need and once you know the attributes you need, often
you'll be using a similar set of attributes most of the time


It is interesting to see in your example that one probeset maps to three
different but closely related genes.  In the past I thought Ensembl would
remove such unambiguous  mappers.  I think the best to do in this case is
to remove all probes that map to multiple genes as there is no way to tell
which gene you'll be measuring.  I'll report this example to the Ensembll
team as they used to do this for us.

Cheers,
Steffen

On Thu, Sep 13, 2012 at 8:29 AM, Juliet Hannah <juliet.hannah@gmail.com>wrote:

> All,
>
> I am trying to create the GSEA chip file. This example uses Affy data,
> and the chip file is already available. I'm
> doing this as an exercise in preparation for other platforms.
>
> The chip file should look like:
>
>
> Probe Set ID    Gene Symbol     Gene Title
> 244901_at       ORF25   hypothetical protein
> 244902_at       NAD4L   NADH dehydrogenase subunit 4L
> 244912_at       CCB382  cytochrome c biogenesis orf382
> 244919_at       CCB203  cytochrome c biogenesis orf203
> 244925_at       NAD7    NADH dehydrogenase subunit 7
>
> How can I obtain the third column from biomart. I tried searching the
> attributes, but couldn't find the right name. Is it a matter of trial
> and error to find the correct attribute, or
> are there systematic ways to find it. Here is what I have so far:
>
> library("biomaRt")
> probeSets <- c("219666_at", "220547_s_at", "218034_at")
>
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
>
> idens <- getBM(attributes = c("affy_hg_u133a","hgnc_symbol"), filters
> = "affy_hg_u133a",values = probeSets, mart = ensembl)
>
>
> Also, does anyone have any suggestions regarding how to handle the
> duplicates (seen in this example) with respect to GSEA.
>
> Thanks,
>
> Juliet Hannah
>
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