Hi Himansha,

I am using GSEA, the java version. I would like to know what other tools
are used for pathway anlaysis.

Wenhuo

On Fri, Apr 13, 2012 at 12:09 PM, <hsharm03@students.poly.edu> wrote:

>
> Dear all,
> This question might sound very naive to most of you but I am new at
> analyzing affymetrix array data using R/Bioconductor packages.
> I have two cel files generated from HT430 Mouse genome. I have to find
> differentially expressed genes in the treated mouse as compared to the
> control.
> For this , I downloaded the "affy" package and got the express set (eset)
> of the differentially expressed genes. I used the rma function to
> normalization , Background correction and differential expression. Now , I
> want to annotate these genes and find out there significance in several
> Pathways. How do I go about doing that?. Also , I read a few topics where
> they say I need to load the library of annotation (ht430mg here). But where
> do I get this database?.
> Any help will be much appreciated as I am new to this topic any sort of
> guidance will be really helpful.
> Thanks,
> Himanshu Sharma.
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>
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-- 


Wenhuo Hu
Park lab

Memorial Sloan Kettering Cancer Center
Zuckerman Research Building
408 East 69th Street
Room ZRC-527
New York, NY 10065
Phone 646-888-3220
huw@mskcc.org

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