[BioC] Needed help on maanova fitmaanova function

[Marcelo Laia]

Hi,

I am run maanova on a set of data and I got a little trouble:

After apply fitmaanova, was showed the message:

Finish gene number 3500 ...
Error in next.fix:(next.fix + ncols - 1) :
        NA/NaN argument

Here is my experiment layout:

Strain = 2 (sensible; tolerant)
Treatment = 2 (inoculated; non inoculated)
Time = 3 (6h, 48h, 120h)
Probes = 3500
Samples = 3
Replicates = 2 (7000 spots)

My script:

mariana.raw <- read.madata("mariana.vns2_ordenado.txt",
                      designfile="design.txt", header=TRUE,
                       spotflag=FALSE,CloneID=1,metarow=2,
                       metacol=3, pmt=4)

mariana <- createData(mariana.raw, 2, avgreps=1, log.trans=FALSE)

model.full.mix <- makeModel(data=mariana, formula=~Var+Trat+
                         Time+Sample+Var:Trat+Var:Time+Trat:Time+
                          Var:Trat:Time, random=~Sample)

anova.full.mix <- fitmaanova(mariana, model.full.mix)

output messages:

Calculating variance components for fixed model...
Fitting mixed effect model...
Finish gene number 100 ...
(...)
Finish gene number 3500 ...
Error in next.fix:(next.fix + ncols - 1) :
        NA/NaN argument
>
> ls()
[1] "abf1.raw"       "mariana"        "mariana.raw"    "mariana.vsn2"
 "model.full.mix"
>
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32

locale:
LC_COLLATE=Portuguese_Brazil.1252;LC_CTYPE=Portuguese_Brazil.1252;LC_MONETARY=Portuguese_Brazil.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Brazil.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"

other attached packages:
 maanova      vsn    limma     affy   affyio  Biobase
 "1.6.0"  "2.2.0" "2.10.5" "1.14.2"  "1.4.1" "1.14.1"
>

Any advice/help is very appreciated!

Thank you very much

-- 
Marcelo Luiz de Laia
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