[BioC] biomart scripting help

[Steffen Durinck]

Hi Marco,

If you use biomaRt in MySQL mode for this query you will get both the 
affy_mouse430_2 and affy_hg_u95av2 ids in the result.
The reason why this doesn't happen in the webservice (default) mode is 
that the BioMart webservice currently doesn't allow this, however I 
expect this to change in the near future.

You'll need to install RMySQL, then try:

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", mysql=TRUE)
mouse=useMart("ensembl", dataset = "mmusculus_gene_ensembl", mysql=TRUE)
homolog = getHomolog( id = c("1939_at","2000_at"), to.array 
="affy_mouse430_2", from.array ="affy_hg_u95av2",from.mart = human, 
to.mart = mouse )

You should get:

 > homolog
       id     MappedID
1 1939_at 1427739_a_at
2 1939_at 1426538_a_at
3 2000_at   1428830_at
4 2000_at   1421205_at


Cheers,
Steffen





marco fabbri wrote:
> I looking for help on biomRt.
> I am starting from a human affy code list and I would like to have the
> mouse homologue.
> If I am running this script I do not know which probe is homologue to
>
>   
>> homolog = getHomolog( id = c("1939_at","2000_at"), to.array =
>>     
> "affy_mouse430_2              ", from.array ="affy_hg_u95av2",
> from.mart = human, to.mart = mouse )
>
>   
>> show(homolog)
>>     
>             V1
> 1 1427739_a_at
> 2 1426538_a_at
> 3   1428830_at
> 4   1421205_at
>
> I also tried with getBM but no success..
> My ideal result would be: from a humann affy id list to get a table like that:
>
> human_probesets -- human_gene_name -- homol_mouse_probesets --
> homolog_mouse_gene_name
>
> Thank Marco
>
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