Hi, I am trying to run an analysis with the package maanova and I am not getting success.
I suppose that I am wrong on set up the formula, so the issue may not be related to R, properly. I have two varieties of plants (V1 and V2). A group of each ones were treated and another was not treated. After treatment, in three different time RNA was collected from treated and from not treated plants for both varieties. So, I have: Var: 2 (varieties) Trat: 2 (treatment) Time: 3 Sample: 3 (biological replicate) Probes: 3575 Spots: 2 for each probe I used the following code: > library(vsn) > todos <- read.matrix("todos_v1_e_v2_back_c.txt",sep="\t") > todos.norm <- vsn2(todos) > write.table(exprs(todos.norm),"todos.norm.txt",sep="\t") > library(maanova) > fabiana.raw <- read.madata("todos.norm.vsn2.maanova.txt", > designfile="design.txt", header=TRUE, spotflag=FALSE,CloneID=1,metarow=2, > metacol=3, pmt=4) > fabiana <- createData(fabiana.raw, n.rep=2, avgreps=1, log.trans=FALSE) > model.full.mix <- makeModel(data=fabiana, > formula=~Var+Trat+Time+Sample+Var:Trat+Var:Time+Trat:Time+Var:Trat:Time, > random=~Sample) > summary(model.full.mix) Model Summary This is a mixed effect model Gene-specific ANOVA model: Var + Trat + Time + Var:Trat + Var:Time + Trat:Time + Var:Trat:Time + Sample Gene-specific Random terms: Sample Gene-specific covariate: None Class Level Information Class Levels Effect 1 Var 2 fixed 2 Trat 2 fixed 3 Time 3 fixed 4 Var:Trat 4 fixed 5 Var:Time 6 fixed 6 Trat:Time 6 fixed 7 Var:Trat:Time 3 fixed 8 Sample 2 random Dimensions Observations(per gene): 36 Columns in X: 24 Columns in Z: 3 Warning message: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, Class, Levels, Effect) (I do no what this warning means. my be the error was here.) > anova.full.mix <- fitmaanova(fabiana, model.full.mix) 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 I was inspecting the files of data and there's nothing wrong close to the probe 3500. Then I calculei the average for each probe in Excel. I tried to perform the analysis again adjusting the option n.rep = 1 and avgreps = 0. There was the same mistake: Finish gene number 3500 ... Error in next.fix:(next.fix + ncols - 1) : NA/NaN argument Then I decided do a permutation on my data and the error continued occurring in the same place: Finish gene number 3500 ... Error in next.fix:(next.fix + ncols - 1) : NA/NaN argument Then I exhausted my knowledge and need a help. Could you suggest me anything here? Thank you very much. -- Marcelo Luiz de Laia ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.