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@uiuc.edu 
	[[alternative HTML version deleted]]

