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

[Marcelo Luiz de Laia]

Dear Gordon and All,

In my laboratory is impossible to have a statistician involved in  anlaysis, now.

My doubt about the normalization with marray appeared due I to have to use limma, after. Then, I thought: Maybe there be a way to enter with the data in marray so that the analyses in limma are easier.

My questions, basically, are:
- Which genes are up-regulated in the three times?
- Which genes are down-regulated in the three times?
- Which are up-regulateds in the time 1 and later they do decrease in the times 2 and 3?
- Which are up-regulateds in the times 1 and 2 and later it does decrease in the time 3?
- Which are down-regulateds in the time 1 and up-regulated  in the times 2 and 3?
- Which are down-regulateds in the times 1 and 2 and up-regulated in the time 3?
I believe that these are the main subjects. Would you have suggestions?

I hope to analyze our data with the help of the members of the list Bioconductor.

Thanks a lot for your interest in help me.

The experiment design is:

                Time
           1day 2day 3day

           Rep1 Rep1 Rep1
Un Treated Rep2 Rep2 Rep2
           Rep3 Rep3 Rep3

           Rep1 Rep1 Rep1
   Treated Rep2 Rep2 Rep2
           Rep3 Rep3 Rep3

Marcelo


Em Tue, 20 Jan 2004 10:42:40 +1100
Gordon Smyth <smyth at wehi.edu.au> escreveu:

GS> At 12:52 AM 20/01/2004, Marcelo Luiz de Laia wrote:
GS> >Hi All,
GS> >
GS> >I have a complex experiment (for me) and I do not known how do I do to 
GS> >normalize it.
GS> 
GS> Why not normalize it exactly has you've normalized data in earlier studies?
GS> 
GS> >More specifically, I don't know as building the file samples (targets) for 
GS> >marray.
GS> >
GS> >The design is:
GS> >
GS> >                 Time
GS> >            1day 2day 3day
GS> >
GS> >            Rep1 Rep1 Rep1
GS> >Un Treated Rep2 Rep2 Rep2
GS> >            Rep3 Rep3 Rep3
GS> >
GS> >            Rep1 Rep1 Rep1
GS> >Un Treated Rep2 Rep2 Rep2
GS> >            Rep3 Rep3 Rep3
GS> >
GS> >If I have one time, my targets file for marrayinput is like this:
GS> >
GS> ># of slide  Names  experiment Cy3  experiment Cy5  date
GS> >1           File1  Un Treated      Treated         19/01/2004
GS> >
GS> >It is a temporary series with three different times and three repetitions 
GS> >in each one of the times.
GS> >
GS> >Me already analysed some simpler experiments. For example, I know to 
GS> >analyse inside of every time, individually. However, I didn't get to find 
GS> >an example alike to mine in the marray vignettes.
GS> >
GS> >After the normalization, I am thinking about using limma.
GS> >
GS> >I would like to know which genes were differentialy expressed in every 
GS> >time. Besides, would I like to verify the behavior of these genes along 
GS> >the time (for example, were they increased or done decreased along the 
GS> >time?). I already had looking at the limma user's guide and I saw that 
GS> >there is the function heatdiagram.
GS> 
GS> Heatdiagram may help you visualize your results, but what you really need 
GS> is the F-statistic computed by the classifyTests() function. This is not 
GS> yet explained in the User's Guide. Can you consult a local statistician for 
GS> help who knows a little about linear models and contrasts?
GS> 
GS> Gordon
GS> 
GS> >I will need to analyze it in the marray in a way that is easier of being 
GS> >analyzed in limma. Another doubt that I already have on limma would be the 
GS> >file design.
GS> >
GS> >All help will be very welcome.
GS> >
GS> >Best wishes.
GS> >
GS> >--
GS> >Marcelo Luiz de Laia, M.Sc.
GS> >Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
GS> >Universidade Estadual Paulista - UNESP
GS> >Via de Acesso Prof. Paulo Donato Castelane, Km 05
GS> >14.884-900 - Jaboticabal, SP, Brazil
GS> >PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
GS> >HomePhone: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com
GS> 


-- 
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