[BioC] normalization and analysis of connected designs

[Ramon Diaz]

Dear All,

Suppose we have an experiment with cDNA microarrays with the structure:

A -> B -> C -> D

(i.e., A and B hybridized in the same array, A with Cy3, B with Cy5; B and C 
in the same array, with B with Cy3, etc).

In this design, and if we use log_2(R/G), testing A == D is straightforward 
since A and D are connected and we can express D - A as the sum of the log 
ratios in the three arrays.

But suppose we use some non-linear normalization of the data, such as loess as 
in Yang et al. 2002 (package marrayNorm) or the variance stabilization method 
of Huber et al., 2002 (package vsn).  Now, the values we have after the 
normalization are no longer log_2(R/G) but something else (that changes with, 
e.g., log_2(R*G)).  Doesn't this preclude the simple "just add the ratios"? 
Is there something obvious I am missing?

Thanks,

Ramón


-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://bioinfo.cnio.es/~rdiaz