[R] Could not find createData function

[Peter Ehlers]

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