[BioC] Problem when comparing a large experimental group versus a small control group by using SAM

[Naomi Altman]

Dear Alex,
You have just rediscovered one of the problems of classical testing - 
when the sample size is large, you have the power to detect 
differences that are statistically significant, but have no practical 
importance.  The answer here is to filter on a threshold of 
differential expression which you consider to be important in 
addition to statistical significance (2-fold is often used) or switch 
to Bayesian methods (e.g. use the Bayes factor).

--Naomi

At 02:40 PM 9/11/2007, Alex Tsoi wrote:
>Dear all,
>
>Currently I am using SAM to identify the differentially expressed genes
>between two groups. The first group has 99 experiments, and the second one
>has around 15 experiments. When I use the SAM to do the analysis, I identify
>so many differentially expressed genes even if I set the FDR threshold to be
>very low. I am just wondering if I should just randomly pick 15 experiments
>from the first group, and to compare the 15 experiments on the second group
>?  or does it matter ?
>
>I greatly appreciate for any comment or advice.
>
>
>Thanks,
>
>
>
>
>--
>Lam C. Tsoi (Alex)
>Medical University of South Carolina
>
>         [[alternative HTML version deleted]]
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111