[BioC] single channel analysis of loop designs
Guilherme J M Rosa
rosag at msu.edu
Wed Jan 4 03:37:49 CET 2006
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.
for some discussion on different levels of replication (technical and
biological), and appropriate modeling of such data structures.
All the best,
> Dear Matthew,
> I guess the main publication is my own - at present only an
> unrefereed conference proceeding.
> 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
Department of Animal Science
Department of Fisheries and Wildlife
Michigan State University
1205-I Anthony Hall
East Lansing, MI
Phone: + 1 517 353-5102
Fax: + 1 517 353-1699
E-mail: rosag at msu.edu
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