[BioC] Help to analyse a complex experiment

[Naomi Altman]

This design is called a 2-way factorial.  If 
these are 2 channel arrays with T1 and T2 on each 
array, this is called a split plot design, with 
Variety as the whole plot treatment.  To do a 
proper analysis, you need to have replicates.

There are many good books on the analysis of 
experiments which do not require lots of 
mathematics.  The texts by Kuehl and by 
Montgomery are very popular, but almost any book 
on experimental design will have this information.

--Naomi

At 09:42 AM 1/23/2006, Marcelo Luiz de Laia wrote:
>Dear Bioconductor users and developers!
>
>We have a complex experiment (for me) and we would like to receive
>suggestions on how to analyse it, if possible.
>
>The design is:
>
>  Var A           Var B        Var C         Var D
>-------------      -------------     -------------     -------------
>T1     T2      T1     T2    T1     T2     T1     T2
>
>Vars A and C are resistant and Vars B and D are susceptible to T1. T2 is
>a controll.
>
>We are interested to get the data from Vars, treatments (T1 and T2) and
>their interactions effects
>
>I do an analysis using limma for each Vars, but, I dont have an ideia
>how I do an analyse for all.
>
>I appreciate any comentary and/or papers suggestions.
>
>The data set are in a matrix after normalization with vsn package.
>
>Thank you
>
>--
>Marcelo Luiz de Laia
>Ph.D Student in Genetics and Plant Breeding
>São Paulo State University (http://www.unesp.br/eng/)
>School of Agricultural and Veterinary Sciences
>Department of  Technology
>Via de Acesso Prof.Paulo Donato Castellane s/n
>14884-900   Jaboticabal - SP - Brazil
>Fone: +55-016-3209-2675
>
>_______________________________________________
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>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111