[BioC] Get Gene annotation (GO terms)

[David martin]

Yes that's correct. I will give Gostats a try !!

thanks.

On 03/17/2011 10:43 PM, Marc Carlson wrote:
> 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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