
Dear list, 
I am mastering myself LIMMA for the analysis of my Affy data. The help of a colleague and the examples in the user guide makes me progress quite well. :)However, I do have a question that is not addressed in the documentation or mail archive that hopefully someone can answer. 
One of the powers of LIMMA is that it applies a moderated t-test (eBayes) in which information of standard errors is borrowed across genes to shrink it for low-expressed genes. 
Q: is this only WHITHIN an array (i.e. columns), but also BETWEEN arrays (i.e. rows)? In other words, the more arrays are present in my eset, the better eBayes works? 
-->  I do have an experiment in which both wildtype and knockout mice are analyzed; for now I am interested in the effects of a nutrient in wildtype mice only. When I omit the KO mice, will that influence the moderated t-test statistics for the wildtype mice (putting aside normalization effects)? 
Thanks for now,
Guido 

 
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
 
tel: (+)31 317 485788
fax: (+)31 317 483342
 
internet:   http://nutrigene.4t.com
email:      guido.hooiveld@wur.nl


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