[BioC] limma(B) and maanova(La.svd) questions

[Aurélie Laugraud]

Hello,
I am working on 2-color arrays, 2 arrays (2 conditions), 27648 spots. my 
first try with maanova was very unsuccessful as
there was an problem with the degrees of freedom ( model contained 
Array+Dye+Sample ...I don't think it is too much but it was). My second 
try was to put Array as random but I got this:
"Fitting mixed effect model...
Erreur dans La.svd(X, method = "dgesvd") : infinite or missing values in 
'x'"
I have no idea what to change to make it happy, I however found out that 
it is very likely the function "pinv" in "mixed" that is unhappy...
Then I tried limma, everything went find and ok until I had a look at 
the "B" value which was terrifyingly low (the best I can get is 0.67 for 
the best score). I tried quite a lot of different values for the 
parameters but it doesn't seem to
change the real underlying problem there.
Does anyone haven any idea or have seen the same things ?

Thanks

Aurélie