[BioC] Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?

[Scott Robinson [guest]]

Dear List,

I am working with Affymetrix's miRNA V1 chip, which uses very different probe sets for different molecule types, e.g. 4 identical probes for one miR, or 11 different probes for a snoRNA.

I have read that the eBayes step assumes equal error variance between probe sets so it is not suitable for this kind of mixed set of probe set designs. To further complicate matters I am thinking about generating a custom CDF where the miR probe sets would have varied number of probes.

http://pomelo2.bioinfo.cnio.es/help/pomelo2-help.html#toc10

Should I look at everything through Limma without the eBayes step (making it equivelant to a normal t-test?), or separate into several different analyses for different molecule types and only drop the eBayes step for the miRs (which will have varying sizes of probe sets)?

Many thanks,

Scott

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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