[BioC] batch effect on variances

[Robert Gentleman]

Lana Schaffer wrote:
> Hi,
> I want to find out if there is a batch effect (FEM or REM) on the variance for 2 sets of
> data which are discrete (different) treatments (time).  The GeneMeta package is designed
> to combine batches which measure the same treatment effects.  However, I have what
> corresponds to 2 different treatment effects.  Is it valid to check homogeneity for the 
> 2 batches?

  Hi,
    You can do some things, but I am not sure why you care? If the two 
experiments do not have the same treatments then there is no sensible 
analysis that combines them, so whether or not the variances are the 
same, seems like an odd question, at least to me.  What would you want 
to say about it and how might you try and use it?

   You can fit an appropriate model to each gene in each experiment 
separately, say using limma or any of the multitude of packages in BioC 
to do this. Once that has been done, you can estimate per gene 
variances, and then their ratio, suitably normalized will almost surely 
follow some form of F statistic (provided that samples are not too small 
and that the models are reasonable).  But I am still not sure what you 
would do with such information.

   best wishes
     Robert


> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
> 
> 
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org