[BioC] Contrast, help

[Marcelo Luiz de Laia]

My apologize for sending off topic to the list.

I, with the help of the user's guide and of the html_help, I set up the following contrast matrix:

> design
  time1 time2 time3
1     1     0     0
2     1     0     0
3     1     0     0
4     0     1     0
5     0     1     0
6     0     1     0
7     0     0     1
8     0     0     1
9     0     0     1
> contrast.matrix <- makeContrasts(time2-time1, time3-time2,time3-time1,levels=design)
> contrast.matrix
      time2 - time1 time3 - time2 time3 - time1
time1            -1             0            -1
time2             1            -1             0
time3             0             1             1

Considering that my experiment relates levels of hidric stress, in other words, in the time zero there is no lack of water and, with the increase of the time, the shortage of water went increasing. Therefore, in the time x, larger than 3 (x>3),  the plants died for lack of water.

I can generate 3 tables of genes, one for the contrast 1, one for the 2 and one for the contrast 3.

My doubt is the following: can I say that the genes of the table 1 are the genes differentialy expressed in the time 1? Can I say that the genes of the table 3 are the genes differentialy expressed in the time 2? same for the time 3?

Maybe I don't know how to formulate a question in English that really characterizes my doubt, therefore, if somebody can explain to me, shortly, an interpretation for this contrast matrix, would be very welcome.

Thanks very much

-- 
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.)
HomePhone: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com