[BioC] sample size for microarray experiments having 2 factors with one random effect

Naomi Altman naomi at stat.psu.edu
Fri Apr 24 04:40:36 CEST 2009

This appears to be a randomized complete block design.  The way I 
would compute the sample size is:

Use a routine that computes sample size for a randomized complete block design.
If you are planning to use log2 expression, then enter "1" as the 
size of the difference you want to detect.  That
corresponds to 2-fold.
Using someone else's data for the same experiment, compute the sd for 
each gene (e.g. using Limma).  Use the 70th or
80th percentile of SD as the SD for computing sample size.  (This 
will be somewhat anti-conservative, but software for RCB
sample size will not include EBayes computations which boost the 
power for any sample size, which is like decreasing the SD.)

Then just enter the p-value and power that you want.  Again, you 
might want to consider using a smaller p-value to adjust for multiple 
If so, you could look at the q-value versus p-value plot for the data 
you used to compute SD, and pick the p-value corresponding to your 
desired q-value.

The number of replicates in any experiment should be at least 
3.  (Those of you working in the medical field will think this is 
ridiculously small, but in underfunded
areas of biology we are happy if we have funds for more than 3 reps.)

There is also software from uab.edu called PowerAtlas.  I haven't 
looked recently, but I think it is primarily for completely randomized designs.


At 10:09 PM 4/23/2009, shirley zhang wrote:
>Dear list,
>I have the following  affymetrix microarray experiment:
>2 fixed effects, each factor has two levels
>1 random effect (patient)
>Can anybody tell me how to calculate the sample size for it?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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

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