[BioC] normalization and analysis of connected designs

[Gordon Smyth]

At 02:27 AM 2/07/2003, Ramon Diaz wrote:
>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?

Yes, you have misunderstood the point of the normalization step, which is 
to bring the log-ratios back to the scale on which the log-ratios have the 
expected linear relationships. If the log-ratios already obeyed the 
relationships such as D-A = AB+BC+CD straight off the arrays then we 
wouldn't normalize!

Gordon

>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
>
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