[BioC] problem with duplicateCorrelation and ExpressionSet objects

[Jenny Drnevich]

Hi Gordon,

Sorry about my confusion in not having usable data in my example. I 
just upgraded to limma 2.10.5, and now duplicateCorrelation() is 
working  fine for ExpressionSets.

Thanks for all your help,
Jenny

At 07:50 PM 5/29/2007, Gordon Smyth wrote:
>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

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