[BioC] maanova error

[Georg Otto]

Dear Bioconductors,

I have a problem using maanova. I try to reproduce the analysis in the
vignette chapter 5.3 ("An affymetrix experiment") using my own data. I
have a time series experiment of developmental stages and I want to
detect genes that change their expression over time. The data are
generated using Affymetrix chips and the expression set is calculated
by RMA.

I generate a file of expression values readable by maanova like this:

>write.exprs(eset, file="expression.txt")

and according to the vignette I read in the data like this:

>data.raw<-read.madata("expression.txt", ID=1, pmt=2, spotflag=FALSE)

at this point I receive a warning that I ignore, since for affymetrix
chips I do not have row and column information:

Warning messages:
1: No meta row information, use 1 instead! in:
   read.madata("expression.txt", ID = 1, pmt = 2, spotflag = FALSE)
2: No meta column information, use 1 instead! in:
   read.madata("expression.txt", ID = 1, pmt = 2, spotflag = FALSE) 
3: No row information. in: read.madata("expression.txt", ID = 1,
   pmt = 2, spotflag = FALSE) 
4: No column information. in: read.madata("expression.txt", ID = 1,
   pmt = 2, spotflag = FALSE)



>data.maanova<-createData(data.raw, 1, log.trans=F)

>model.full.mix<-makeModel(data=data.maanova,
        formula=~Stage+Sample, random=~Sample)


>anova.full.mix<-fitmaanova(data.maanova, model.full.mix)

in the next step, which is the F-test, I get an error:


> test.Stage.mix<-matest(data.maanova, model.full.mix, term="Stage",
  n.perm=100)
Doing F-test on observed data ...
Error in var(log(Chis)) : missing observations in cov/cor
In addition: Warning message:
NAs produced in: rchisq(n, df) 


My question is: what is wrong here? Where do the missing observations
and the NAs come from? As far as I know, my original expression set
does not have NAs.  How can I find missing observations or NAs in a
dataset? And more general: How can I circumvent this problem?

I am running the devel version of maanova:

Package: maanova
Version: 0.98.8
Built: R 2.1.1; powerpc-apple-darwin7.9.0; 2005-09-14 15:01:52; unix


Thanks a lot for your help!

Georg