[BioC] Needed help on maanova fitmaanova function

[Marcelo Laia]

Hi,

An update for my previous message.

I did a mistake, sorry!

We have 3575 probes duplicated two times (7150 spots)

I averaged our data manually, and the script stop in the same gene: 3500

Here is the rows 3499, 3500 and 3501, after averaged

> mariana.raw$data[3499:3501,]
           [,1]     [,2]      [,3]        [,4]      [,5]     [,6]
 [,7]      [,8]       [,9]     [,10]
[1,]  2.8799185 3.928514  3.832121  1.64066911 0.6918954 1.832052
3.9312625 3.4691186  3.9743854 2.9595916
[2,]  1.1528810 2.059948  1.922955 -0.06229394 0.3844479 1.976129
1.7131545 1.8113138  2.3615181 0.8506805
[3,] -0.1713525 1.794244 -1.215398 -0.20845209 0.8610410 1.536862
-0.6310796 0.0691264 -0.2944953 0.7377530
          [,11]        [,12]       [,13]    [,14]      [,15]
[,16]      [,17]      [,18]      [,19]
[1,]  3.0119187  2.557758428 2.537979355 1.891655  0.5448964
4.33738414  3.8543186  2.8559283  2.7103026
[2,]  0.2379391 -1.319239837 0.997866769 1.428783 -0.1927725
2.04550902  2.0779253  1.5854125  0.7298848
[3,] -1.7515767  0.007996354 0.002550649 2.514868  1.8652844
-0.05730803 -0.3170056 -0.4108894 -0.1207585
         [,20]     [,21]      [,22]    [,23]    [,24]      [,25]
[,26]     [,27]     [,28]       [,29]
[1,] 2.4974726 0.6478784  2.2628555 2.028872 2.194005  4.0899848
4.96797046 4.8208710 2.3931935  1.07063777
[2,] 0.3580076 0.7686108  0.8717802 1.659451 2.113730  1.6449902
2.26602230 2.2739086 1.0512341 -0.16315782
[3,] 0.4198082 0.1423484 -1.3532243 1.295030 1.836653 -0.5125613
-0.04661076 0.5556742 0.1747772 -0.04557642
          [,30]      [,31]      [,32]      [,33]      [,34]      [,35]     [,36]
[1,]  0.7829148  2.2246866  3.1774726  1.5472313  4.6552379  5.1588851 1.0682432
[2,] -0.2742727 -0.4904089 -2.4227434 -0.6602519  2.4540085  2.0049234 0.9844796
[3,]  0.0890056  0.5101666  0.1555357  0.8493551 -0.9342303 -0.2179986 1.0333517
>

Any help is very, very welcome.

Thank you very much

Marcelo

2007/8/2, Marcelo Laia <marcelolaia at gmail.com>:
> 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