[BioC] A question about multiple analysis

[Gordon Smyth]

At 02:38 AM 16/11/2003, Marcelo Luiz de Laia wrote:
>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.

I am assuming that you have made microarrays which compare treated and not 
treated samples for each of the varieties individually, but that you have 
no microarrays which compare samples from two different varieties. If this 
is correct, then limma does not allow you to compare the two varieties. I 
don't know of any software in Bioconductor which allows you to do this, at 
least not at this time.

What you need is sometimes called a "single-channel" analysis. You could 
try the mixed model method implemented in R/maanova from Gary Churchill's 
lab site

http://www.jax.org/staff/churchill/labsite/software/index.html

You might consider using normalizeBetweenArrays() in limma before exporting 
you data to maanova.

Even using single-channel software, comparisons between varieties will be 
intrinsically noisier than comparisons between treated and untreated, 
because you didn't design these comparisons into your experiment.

Gordon

>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