[R] Help needed to analyse a factorial microarray experiments! Newbie Question

[Leonardo Boava]

Dear R-users:

I am using the package MAANOVA to analyze microarray data and have
encountered problems when trying to get interactions.

I am a newbie in both, R and maanova, and I do not have good knowledge in 
statistical methods.

I have four effects:

Effects   Levels
Var      2
Ind      2
Trat     2
Time     4
Sample   3 <-- biological replicate
Spot     4 <-- technical replicate

I had fitted a model to got all interactions with Samples in random effect 
(mixed). But, I got an error when I include the Var:ind:Trat and Var:ind:Time 
in the fitted model. May be I didn't had degree of freedom enough.

Then I did an analyses without those interactions (Var:ind:Trat and 
Var:ind:Time ).

Now, I would like to known if are possible to get the interactions with three 
factors and interactions with four factors.

I am interested in known which genes are differentially expressed in Var 1, 
Ind 2, Trat 1 , Time 3, for example.

Could you address me how do I could do that?

If I include the technical replicate in the model, can I get those 
interactions?

If you had analysed a experiment like this, could you share your script?

Does anyone have experience using MAANOVA commands and is willing to help?

Any comments are very welcome!

Thank you very much.

Leonardo