[BioC] A question about multiple analysis

[Marcelo Luiz de Laia]

Hi All

I analyzed an experiment using marrayNorm to normalize the data and limma to
verify the differentialy expressed genes.

The experiment is composed for two varieties of plants, susceptible and
resistant, to a phytophatogenic microorganism. Each one of the two varieties
was divided in two groups, treated (experiment) and not treated (control).
Therefore, we have the following layout:

resistant   |-> not treated
          ->|
variety     |-> treated


susceptible |-> not treated
          ->|
variety     |-> treated

As I said above, I only analyzed inside (treat x not treated) of each
variety.

I would like to know if is possible to verify the differentialy expressed
genes between the varieties, or either, to compare the susceptible variety
with the resistant variety, using Bioconductor and R.

How I could make this? To compare treated susceptible variety with treated
resistant variety? Or to compare not treated susceptible variety with not
treated resistant variety? Or both?

Thanks


Marcelo Luiz de Laia, M.Sc.
Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
Universidade Estadual Paulista - UNESP
Via de Acesso Prof. Paulo Donato Castelane, Km 05
14.884-900 - Jaboticabal, SP, Brazil
PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com
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