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

[Gordon Smyth]

At 12:52 AM 20/01/2004, Marcelo Luiz de Laia wrote:
>Hi All,
>
>I have a complex experiment (for me) and I do not known how do I do to 
>normalize it.

Why not normalize it exactly has you've normalized data in earlier studies?

>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.

Heatdiagram may help you visualize your results, but what you really need 
is the F-statistic computed by the classifyTests() function. This is not 
yet explained in the User's Guide. Can you consult a local statistician for 
help who knows a little about linear models and contrasts?

Gordon

>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