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

[Gordon Smyth]

At 11:20 PM 20/01/2004, Marcelo Luiz de Laia wrote:
>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.

You can enter your data in marraInput or using limma. It makes no 
difference for the analysis. It's simply a matter of what you find easiest 
to use.

Gordon

>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