[BioC] [maNorm] Normalization a complex experiment...

[Marcelo Luiz de Laia]

Hi All,

I have a complex experiment (for me) and I do not known how do I do to normalize it.

More specifically, I don't know as building the file samples (targets) for marray.

The design is:

                Time
           1day 2day 3day

           Rep1 Rep1 Rep1
Un Treated Rep2 Rep2 Rep2
           Rep3 Rep3 Rep3

           Rep1 Rep1 Rep1
Un Treated Rep2 Rep2 Rep2
           Rep3 Rep3 Rep3

If I have one time, my targets file for marrayinput is like this:

# of slide  Names  experiment Cy3  experiment Cy5  date
1           File1  Un Treated      Treated         19/01/2004

It is a temporary series with three different times and three repetitions in each one of the times.

Me already analysed some simpler experiments. For example, I know to analyse inside of every time, individually. However, I didn't get to find an example alike to mine in the marray vignettes.

After the normalization, I am thinking about using limma.

I would like to know which genes were differentialy expressed in every time. Besides, would I like to verify the behavior of these genes along the time (for example, were they increased or done decreased along the time?). I already had looking at the limma user's guide and I saw that there is the function heatdiagram.

I will need to analyze it in the marray in a way that is easier of being analyzed in limma. Another doubt that I already have on limma would be the file design.

All help will be very welcome.

Best wishes.

-- 
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