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.
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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
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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
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