[BioC] single channel analysis of loop designs

[Guilherme J M Rosa]

Dear Matthew and Naomi: 

You may be interested also on taking a look at: 

G. J. M. Rosa, J. P. Steibel, R. J. Tempelman (2005) Reassessing design and 
analysis of two-colour microarray experiments using mixed effects models. 
Comparative and Functional Genomics 6(3): 123-131.
http://www3.interscience.wiley.com/cgi-bin/jissue/110473749 

for some discussion on different levels of replication (technical and 
biological), and appropriate modeling of such data structures. 

All the best, 

Guilherme. 

> Dear Matthew,
> I guess the main publication is my own - at present only an 
> unrefereed conference proceeding. 
> http://www.stat.psu.edu/%7Ewzhao/bcc/respapers/AltmanInterface04.doc
>   I think that the Kerr and Churchill papers do it this way, too, but 
> they do not explain why. 
> 
> Basically, using differences has 2 disadvantages - it has higher 
> variance than single channel analysis, and if a spot is missing on an 
> array, many of the effects for that gene cannot be estimated.

--  

Guilherme J. M. Rosa
Assistant Professor
Department of Animal Science
Department of Fisheries and Wildlife 

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824-1225 USA 

Phone: + 1 517 353-5102
Fax: + 1 517 353-1699
E-mail: rosag at msu.edu
http://www.msu.edu/~rosag/