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_M ONETARY=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 S?o 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

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_Brazi l.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 S?o 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