[BioC] problem with duplicateCorrelation and ExpressionSet objects

[Gordon K Smyth]

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