[BioC] limma Factorial 2x2x2x4 : Did I a correct parametrization ?

[Marcelo Laia]

Dear Bioconductors Friends!

I did a parametrization, based on 8.7 Factorial Designs section on
limma usersguide, in a 2x2x2x4 factorial experiment and I would like
to ask you if I did a correct script for limma.

Here is my targets file:

   http://www.divshare.com/download/3986449-8af

And here is my script file:

   http://www.divshare.com/download/3986693-8ea

My doubts are on how to I could interpret the topTable out put based
on my contrasts!

--- topTable(fit2,coef=1,number=10)
coef=1 = Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0

Here are the genes which respond to Inoc on Time 0, Sus, and H20.
There aren't interactions here. True? The genes up- or down-regulated
in topTable are up or down-regulated in "Sus.H2O.Inoc.0" or in
"Sus.H2O.Ctrl.0"?

--- topTable(fit2,coef=17,number=10)
coef=17 = (Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0)

Here are the genes which respond to BION and Inoc on Sus and Time 0,
or here are the interaction between BION and Inoc (Var:Ind) on Sus and
Time 0. True? The genes up- or down-regulated in topTable are up or
down-regulated in "(Sus.BION.Inoc.0-Sus.BION.Ctrl.0)" or in
"(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0)"?

--- topTable(fit2,coef=25,number=10)
coef=25 = ((Res.BION.Inoc.0-Res.BION.Ctrl.0)-(Res.H2O.Inoc.0-Res.H2O.Ctrl.0))-((Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0)),

Here are the genes which respond to Res and BION and Inoc on Time 0,
or here are the interaction between Res and BION and Inoc
(Var:Ind:Trat) on Time 0. True? The genes up- or down-regulated in
topTable are up or down-regulated in
"((Res.BION.Inoc.0-Res.BION.Ctrl.0)-(Res.H2O.Inoc.0-Res.H2O.Ctrl.0))"
or in "((Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0))"?

Could I extract all interactions?

May be that this are basics questions, but I am very insecure with
they. Could you suggest anything here?

Thank you so much!

-- 
Marcelo Luiz de Laia
Jaboticabal - SP - Brazil
sip:marcelolaia at ekiga.net

"Você vê as coisas como elas são e pergunta: por quê? Mas eu sonho com
coisas que nunca foram e pergunto: por que não? " - Bernard Shaw