[BioC] Spot duplicate in timecourse package and "missing" values

[Marcelo Laia]

Hi,

My cDNA array have 2 duplicate for each spot.

I read and normalize my data set in limma.

I use the result MAList (MA) object in timecourse package.

But, I get a error:

> out1 <- mb.long(MA.2, times = 3, reps = size)
Time group assignments are set to default.
Replicate group assignments are set to default.
Erro em mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, time.grp,  :
        890 genes may have missing values in some of the replicates.

If I use method="normexp" in backgroundCorrect function in limma, the
error disappear. But, I would like to use the method="subtract". Do
timecourse package handle NAs?

In this array I have controls (DMSO and spike, around 1000 spots) and
I flagged they, then I use wt.fun=function(x) as.numeric(x$Flag==0) to
exclude they in read.maimages function.

Could you advice me to solve this problem, if it is possible to solved?

Thank you very much

-- 
Marcelo Luiz de Laia
Ph.D Candidate
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof. Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Phone: +55-016-3209-2675
Cell: +55-016-97098526