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Dear Sam,

I am working with Microarray Data analysis for illumina's WG-DASL assay
based Human sample.
Actually I want to know Gene-Gene interaction between my differentially
expressed genes.

Thanks,
Abdul Rawoof


_________________________________________________________________________________


Abdul,
   When you say gene-gene interaction, what exactly do you mean?  Are you
looking for protein-protein binding data for your DE genes?  Or are you
after other genes that have been shown to (or may) be co-regulated?

There are many ways to do analysis, and everything has pros and cons, and
if you aren't careful your analysis will mean nothing because you applying
the wrong method/models.  In order to answer your question, we must know
exactly what you want to do and find out.  Integrated network analysis and
gene-gene interaction can have several interpretations.  Please, be verbose

Best,



On Tue, May 7, 2013 at 9:59 AM, Sam McInturf <smcinturf@gmail.com> wrote:

> Abdul,
>    Can you tell more about your project and what exactly you mean
> by integrated network analysis.  What are you integrating into your DE
> genes?  what organism are you working with?  What are you trying to find in
> the data.  Is the data RNA seq or micro array (and which platform).
>
> bioconductor has many packages that you can use to handle networks, but
> the `best` package depends on your goals / aims / resources.
>
> Best
>
>
> On Tue, May 7, 2013 at 5:57 AM, Abdul Rawoof <abdul87.edu@gmail.com>wrote:
>
>> Hello,
>>
>> I want to do an intergrated network analysis for my Differential Expressed
>> genes. So could anyone tell me how can I do. Which package should I use.
>>
>> Thanks,
>> Abdul Rawoof
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>
>
> --
> Sam McInturf
>



-- 
Sam McInturf

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