[BioC] problem with duplicateCorrelation and ExpressionSet objects

[Gordon Smyth]

Dear Jenny,

I have double-checked by re-installing limma 2.10.4 from 
Bioconductor, and it seems that I failed to commit all the necessary 
files to the Release branch. My apologies. I have now committed limma 
2.10.5 which should be correct and complete.

I append a small reproducible example to show that the problem is 
fixed in limma 2.10.5.

Best wishes
Gordon

 > library(Biobase)
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

 > library(Matrix)
Loading required package: lattice
 > library(limma)
 > x <- matrix(rnorm(100*4),100,4)
 > y <- new("ExpressionSet",exprs=x)
 > cofit <- duplicateCorrelation(y,ndups=1,block=c(1,1,2,2))
Loading required package: statmod
 > sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" 
"utils"     "datasets"  "methods"   "base"

other attached packages:
     statmod       limma      Matrix     lattice     Biobase
     "1.3.0"    "2.10.5" "0.99875-1"    "0.15-5"    "1.14.0"

At 02:58 AM 30/05/2007, Jenny Drnevich wrote:
>Hi Gordon,
>
>I think I've gotten a reproducible example - below is an entire R 
>session. I cut down the packages I had loaded to only those 
>necessary (except for RWinEdt, but I also tried it without and the 
>same thing happens). If I only load gcrma and limma (+ 
>dependencies), duplicateCorrelation works fine on an ExpressionSet 
>object. However, if I load Matrix, then it doesn't work, so somehow 
>there's still a conflict with the Matrix NAMESPACE? Let me know if I 
>need to try anything else...
>
>Jenny