[BioC] Reg: GSEA

[Marc Carlson]

Hi Rohit,

Yes.  You can definitely test KEGG terms.  But be sure you have the very
latest version of the Category package.  In the current release this
would be 2.12.1


  Marc



On 04/19/2010 03:12 AM, Rohit Farmer wrote:
> Thanks Andreia ...
>
> This GOstats package will also work with KEGG database pathway data or
> i have to use another package and there is one more package i found
> that is GSEAbase ... so which one is better or can say easy to use and
> implement ...
>
> Thanks
>
> rohit
>
> On 4/19/10, Andreia Fonseca <andreia.fonseca at gmail.com> wrote:
>   
>> Dear Farmer,
>>
>> you can use GOstats package.
>> regards,
>> Andreia
>>
>> On Mon, Apr 19, 2010 at 10:59 AM, Rohit Farmer
>> <rohit.farmer at gmail.com>wrote:
>>
>>     
>>> Hello everyone ...
>>>
>>> I just did a moderate t statistics using limma package and found out a
>>> list of genes which are differentially expressed now i wan to go for
>>> gene set enrichment analysis using GO terms and pathway analysis ...
>>> so can anyone suggest me the bioconductor packages which i can use for
>>> the same ..
>>>
>>> Thanks and regards
>>>
>>> Rohit
>>> --
>>> Rohit Farmer
>>> M.Tech Bioinformatics
>>> Department of Computational Biology and Bioinformatics
>>> Jacob School of Biengineering and Biotechnology
>>> Sam Higginbottom Institute of Agriculture, Technology and Sciences
>>> (Formerly known as Allahabad Agricultural Institute - Deemed University)
>>> Allahabad, UP, INDIA - 211 007
>>> Ph. No. 9839845093, 9415261403
>>> e-Mail rohit.farmer at gmail.com
>>> Blog http://rohitsspace.blogspot.com
>>>
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>>>       
>>
>> --
>> --------------------------------------------
>> Andreia J. Amaral
>> Unidade de Imunologia Clínica
>> Instituto de Medicina Molecular
>> Universidade de Lisboa
>> email: andreiaamaral at fm.ul.pt
>>          andreia.fonseca at gmail.com
>>
>>     
>