[BioC] r/maanova error in matest()

[Mike Walter]

Dear List,

I'd like to use maanova to analyze a set of 64 affy arrays (U219). The samples are from 8 donors (4x male and female each), which where taken in a short timecourse (T0-T3) both treated and untreated. I'm interested transcripts that are affected by the treatment and especially in those that react differently in male and female samples. The code I used to fit the anova model was: 

> anova.in = read.madata(exprs(data.filt), designfile=designfile)> fit = fitmaanova(anova.in, + formula = ~time+treat+gender+donor+time*treat+time*gender+treat*gender,+ random = ~donor)

However, when I like to extract transcripts, that are e.g. changing over time I have following error: 

> ftest.time = matest(anova.in, fit, term="time", test.method= c(0,1), + test.type="ftest", shuffle.method="sample", n.perm=500)Error: No degree of freedom to do the test

When I repeat the analysis with a fixed model (skipping the donor in the formula) I have the same problem.
So I'd would appreciate any help on how to correctly build the formula to be able to extract the DE genes.

Thank you very much in advance,

Mike



Session Info:

R version 2.12.0 (2010-10-15)Platform: i386-pc-mingw32/i386 (32-bit) locale:[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages:[1] stats graphics grDevices utils datasets methods base other attached packages:[1] affy_1.28.0 Biobase_2.10.0 maanova_1.20.0 loaded via a namespace (and not attached):[1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0