[BioC] Get Gene annotation (GO terms)

[Marc Carlson]

Unless you meant that you are intending to do hypergeometric testing, 
(which is a different question).  If that was your question, then 
GOstats works well, although there are indeed many to choose from.

   Marc



On 03/17/2011 02:40 PM, Marc Carlson wrote:
> Hi David,
>
> For human you want to use org.Hs.eg.db.
>
> Other packages may also contain GO terms but not mapped onto the 
> correct set of genes.  So if instead you had used org.Mm.eg.db, you 
> would find GO terms mapped only onto mouse genes and symbols.
>
>
>   Marc
>
>
>
> On 03/17/2011 02:21 PM, David martin wrote:
>> Perfect it's human,
>> I guess i can then use any of the GO packages to get signficant 
>> Goterms. Which one would you suggest ?
>>
>> On 03/17/2011 10:16 PM, Marc Carlson wrote:
>>> What species? Those look like human gene symbosl, so I will give an
>>> example for that:
>>>
>>> library(org.Hs.eg.db)
>>> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2")
>>> ## Then you can just merge together the GO to entrez gene mappings with
>>> the SYMBOL to entrez gene mappings like this:
>>> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x=
>>> "gene_id", by.y="gene_id")
>>>
>>> Does that make sense?
>>>
>>>
>>> Marc
>>>
>>>
>>> On 03/17/2011 02:11 PM, David martin wrote:
>>>> Hi,
>>>> Which package should i use to convert a list of gene names
>>>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get
>>>> a list of significant GO terms based on the input genes).thanks for
>>>> pointing me to right direction.
>>>>
>>>> thanks,
>>>> david
>>>>
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>>
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