Dear Jenny,
limma already has an as.matrix method for ExpressionSet objects. I've
just run the following code
which demonstrates that duplicateCorrelation() does work on such
objects:
> library(Biobase)
> library(limma)
> x <- matrix(rnorm(50*4),50,4)
> y <- new("ExpressionSet",exprs=x)
> dupcor <- duplicateCorrelation(y,ndups=2)
Loading required package: statmod
> dupcor$consensus
[1] -0.07112392
I suspect that your data object is not actually an ExpressionSet
object, although perhaps it is
something which inherits from ExpressionSet. I can't tell from your
code where you object has
come from or what class it is.
Because as.matrix() is an S3 generic, there is a problem with S4
objects which inherit from
ExpressionSet. Can you give more information about how your problem
arises?
Best wishes
Gordon
On Thu, May 17, 2007 5:15 am, Jenny Drnevich wrote:
> Hi Gordon and others,
>
> I just tried calling duplicateCorrelation on an ExpressionSet object
> with the newest versions of R, Bioconductor and limma (codes and
> sessionInfo() below) and it won't work. I don't think the problem
> lies with duplicateCorrelation() itself, rather that as.matrix()
does
> not work for ExpressionSet objects whereas it did work for exprSet
> objects. The help file for duplicateCorrelation has this description
> for the input object:
>
> "a numeric matrix of expression values, or any data object from
which
> as.matrix will extract a suitable matrix such as an
> <mk:@msitstore:c:\progra~1\r\r-25~1.0\library\limma\chtml\limma.chm: :="" malist.html="">MAList,
> marrayNorm or exprSet object."
>
> The code and error:
>
> > corfit <-
> duplicateCorrelation(gcrma.pres,design,ndups=1,block=c(2,2,1,1,3,3))
> Error in as.vector(x, mode) : cannot coerce to vector
>
> From debugging duplicateCorrelation, the problem is in the very
> first line of code:
>
> Browse[1]> M <- as.matrix(object)
> Error in as.vector(x, mode) : cannot coerce to vector
>
>
> If you don't intend as.matrix() to work for ExpressionSet objects,
> then the code for duplicateCorrelation maybe should be changed. Of
> course, the easy work-around is to pass exprs(gcrma.pres) to
> duplicateCorrelation.
>
> Cheers,
> Jenny
>
> > sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices"
"utils"
> [7] "datasets" "methods" "base"
>
> other attached packages:
> hgu133plus2probe hgu133plus2cdf affyQCReport geneplotter
> "1.16.0" "1.16.0" "1.14.0" "1.14.0"
> RColorBrewer simpleaffy made4 scatterplot3d
> "0.2-3" "2.10.11" "1.10.0" "0.3-24"
> ade4 affyPLM affydata affycoretools
> "1.4-3" "1.12.0" "1.11.2" "1.8.0"
> annaffy xtable gcrma matchprobes
> "1.8.1" "1.4-3" "2.8.0" "1.8.0"
> biomaRt RCurl XML GOstats
> "1.10.0" "0.8-0" "1.7-1" "2.2.1"
> Category Matrix lattice genefilter
> "2.2.2" "0.9975-11" "0.15-4" "1.14.1"
> survival KEGG RBGL annotate
> "2.31" "1.16.0" "1.12.0" "1.14.1"
> GO graph limma affy
> "1.16.0" "1.14.0" "2.10.0" "1.14.0"
> affyio Biobase RWinEdt
> "1.4.0" "1.14.0" "1.7-5"
> >
>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
