[BioC] r/maanova error in matest()--post scriptum

[Michael Walter]

Hi all,

In case it is important: when fitting the model I get some warnings:

Warnmeldungen:1: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch2: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch3: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch4: In any(parsed.formula$random) :wandle Argument des Typs 'double' nach boolesch5: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch6: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch7: In any(result$random[idx.mainterm]) :wandle Argument des Typs 'double' nach boolesch8: In any(parsed.formula$random) :wandle Argument des Typs 'double' nach boolesch


Kind regards,

Mike

-----Ursprüngliche Nachricht-----Von: "Mike Walter" 
Gesendet: 17.03.2011 11:02:49An: bioconductor at r-project.org
Betreff: [BioC] r/maanova error in matest()>>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
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