[BioC] how to run SAM analysis

[Adaikalavan Ramasamy]

Your design is seriously unbalanced and under-powered. I would suggest
you increase the sample size in the normal group. This holds no matter
what test statistics you plan on using.

LIMMA would probably be better for your purposes. I _think_ it has been
shown empirically to hold for small sample sizes.

Regards, Adai



On Wed, 2005-08-31 at 19:22 -0700, weinong han wrote:
> Hi, List,
>  
> I have 17 affymetrix .cel files and ran RMA analysis on them. Now I want to run SAM analysis(unpaired, 3 normal tissues and 14 diseased tissues)  on the RMA data with R2.1.1. 
> I have installed the samr package. 
>  
> Questions: How to run the SAM analysis after the RMA analysis? The better, the more detailed explanations.
>  
> Any advice and suggestions will be much appreciated.
>  
> 
> 
> 
> Best Regards
>  
> Han Weinong  
> hanweinong at yahoo.com
> 
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