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

[James W. MacDonald]

Hi Daren,

At the very least you will need the affy package. For differential 
expression there are many choices depending on the experimental design. 
For simple comparisons you can use things like multtest or siggenes (or 
even rowttests() in Biobase). For more complex comparisons you might 
want to use limma.

For GO analysis you can use GOstats or topGO.

And <shameless plug> you could use affycoretools to (possibly) make your 
life easier </shameless plug>.

The relevant biocViews page is here:

http://www.bioconductor.org/packages/release/OneChannel.html

Best,

Jim



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. 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662