Hi -- On 07/06/2010 03:21 AM, shabnam k wrote: > Hi, > > I am using "*Maanova* package" to do anova. I have created *datafile* with > probeID as the first column, which is a tab limited text file and also > created *designfile*. I have created *readma object* which is named as abf1. >>From that readma object, i have to create data object by using > *createData*function and also i hav to create model object by using > *makemodel* function, then i have to fit the model of anova.But, the problem > is it could not find createData function. Am pasting the commands which i > used below.Please give me the solution to my problem, as am unabl;e to > proceed further.
maanova is a Bioconductor package so please ask on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html The vignette for this package browseVignettes('maanova') does not mention createData; what instructions are you following? Martin > > > R version 2.11.1 (2010-05-31) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> library(maanova) > > Attaching package: 'maanova' > > The following object(s) are masked from 'package:base': > > norm > >> abf1.raw <- read.madata("gcrmadata.expr. > dat", designfile="design.dat", > + probeID=1, pmt=2, spotflag=F) > Reading one color array. > Otherwise change arrayType='twoColor' then read the data again > Warning messages: > 1: In read.madata("gcrmadata.expr.dat", designfile = "design.dat", : > Assume that the first column is probeid. If you have probeid specify it, > otherwise set 'probeid=0' then read the data again > > 2: In read.madata("gcrmadata.expr.dat", designfile = "design.dat", : > Assume that intensity value is saved from the second column. Otherwise > provide 'intensity' (first column storing intensity) information, and read > the data again > >> abf1.raw > > Summary for this experiment > > Number of dyes: 1 > Number of arrays: 4 > Number of genes: 8799 > Number of replicates: 1 > Transformation method: None > Replicate collapsed: FALSE >> data(abf1) >> abf1 <- *createData*(abf1, 1, log.trans=F) > *Error: *could not find function* "createData" > > > > > * > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ 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.
