[BioC] Advice on how to compare two different sources on cDNA

[Marcelo Laia]

Hi,

I would like to compare 2 RNA sources to see if a culture medium
mimetic the plant host.

There are evidence that a culture medium mimetic the plant, then I
inoculated the phytopatogenic bacteria in both, mimetic culture medium
and plant. After 24 hours, I was collected the RNA and did a 3
hibridizations:

Cy3                                  Cy5
mimetic culture medium vs NA
mimetic culture medium vs NA
mimetic culture medium vs NA

Cy3      Cy5
plant vs NA
plant vs NA
plant vs NA

NA = poor culture medium

I have hybridized they separated because I will use it in a time
course experiment.

I thinking to do a contrast like limma usersguide (11.5 Weaver Mutant
Data: A 2x2 Factorial Experiment).

If the mimetic medium is true (mimetic the plant) I don't will get any
differentially expressed genes. This aproach is good or you suggest me
other?

Thank you very much

-- 
Marcelo Luiz de Laia
Ph.D Candidate
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
Phone: +55-016-3209-2675
Cell: +55-016-97098526