[BioC] At a loss on new project with Affymetrix U133 2.0

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Oct 29 14:53:16 CET 2008


On Oct 29, 2008, at 9:21 AM, Daren Tan wrote:

> I am starting a new project using Affymetrix U133 2.0, and hope to  
> seek suggestions on completing the analysis within 1 to 2 months.  
> The objective is to identify differentially expressed genes, and to  
> perform gene ontology analysis. Now I am at a loss given the diverse  
> packages and algorithms to choose from.

The affy - Primer vignette and the limma user's are as good of a place  
to start as any, I reckon.

Although the limma user's guide has a lot to do with two-color array  
analysis, I'm sure it'll be generally helpful, but also Section 7.2  
talks directly to dealing with affy and other "single channel designs".

To get to the affy vignettes, just:

R> library(affy)
R> openVignette()

And chose the number associated to "Primer" -- reading through all of  
those documents couldn't hurt though :-)

To get the limma user's guide:

R> library(limma)
R> limmaUsersGuide()


Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University


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