[BioC] edgeR query

[Steve Lianoglou]

Hi Shravanthi,

On Tue, Sep 4, 2012 at 6:33 AM, Shravanthi P <shravanthipsg at gmail.com> wrote:
> I am new to using R and my project is on differential gene expression .I
> was told to use Edger but I am having trouble reading a tab delimited
> format data for affy oligonucleotide microarray data .
> How can I read the data into R ? and how can I identify the upregulated and
> downregulated genes  ?

The bad news is that you've got a long way to go before you can get
from where you are to where you want to be. The good news is that
there are a lot of resources available for your self study that can
help you get to where you want to be.

It would be in your best interest to learn more about R first (start
with an intro to R) before you try to do anything more serious.

After you do that, and you then read the (very helpful) edgeR user
manual (as Wenhuo already suggested) -- you'll probably come to the
realization that edgeR is the wrong tool for this job. You have
microarray data and edgeR is used for sequencing data.

In this case, you'll find that the limma package is probably what
you're after. Fortunately for you, there is a very thorough limma user
guide that you can read through that gives you some idea of how to
process different types of microarray data. The goods at the link
below (and the associated packages) are worth some study as well:

http://bioconductor.org/help/workflows/oligo-arrays/

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact