[BioC] How to determine sample size for second-stage experiments

Kort, Eric Eric.Kort at vai.org
Thu Jan 26 19:20:17 CET 2006

Qunyuan Zhang writes....
> Hi,
> We just finished an initial inverstigation (50000-gene Affymetrix, 15
> cancered people and 10 normal people). 40 genes' RNA expressional
> were found significantly different between the two groups (by two
> t tests, p values corrected). We are now planning a second-stage
> experiment to validate this finding. We want to do power analysis and
> sample size calculation, especially want to know how many peoples
> be included in the second-stage experiment.
> Besides the function  Power.t.test(), is there any other functions in
> any packages availabe in bioConductor for this kind of experimantal
> design problems?

It depends how you intend to summarize your data.  Will you be
calculating some type of summary score based on the expression of these
40 genes?  If so, you can easily perform a power calculation based on
the expected means and standard deviations as estimated by your initial
experiment.  Or will you test each of the 40 genes independently?  In
that case, you will need to take into account some type of multiple
comparisons adjustment (e.g. bonferroni, etc.).

> Thanks,
> Qunyuan Zhang
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