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. 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.rawSummary 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]]
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 at 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
On 2010-07-06 4:21, 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. > > > 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" >I think that you're using code from an ancient demo file with a more recent version of maanova. There used to be a createData() function and read.madata used to have arguments 'probeID' and 'pmt', but those are now 'probeid' and, I think, 'intensity'. Try the demo in your (*unstated*) version of maanova. -Peter Ehlers