[BioC] Evaluating differentiall expressed genes

[Sean Davis]

On 12/7/05 12:49 PM, "Tim Smith" <tim_smith_666 at yahoo.com> wrote:

> Hi all,
>    
>   A newbie to Bioconductor, so please forgive the naive question..
>    
>   I had two sets of data (normalized affy data). The first set contains
> cancerous expression data for 40 patients, and the second set contains
> expression data for 30 'normal' (i.e non cancerous) patients.
>    
>   I wanted to find out the genes that are 'differentially expressed' in the
> two sets. Which package, and which functions can I use? Any reasonably popular
> method/package would work for me.

Welcome to bioconductor.

See here for a full list.  Best to do a little reading, as each method has
potentially different assumptions, etc.

http://www.bioconductor.org/packages/bioc/1.7/src/contrib/html/

That said, look at siggenes which contains the SAM method; the multtest
package for traditional t-tests; and the limma package.

And just to be sure, when you say you have two sets of normalized data, you
mean that they were normalized together or separately?

Sean