[BioC] problem with duplicateCorrelation and ExpressionSet objects
drnevich at uiuc.edu
Wed May 30 21:49:11 CEST 2007
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,
At 07:50 PM 5/29/2007, Gordon Smyth wrote:
>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.
> > 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)
>attached base packages:
> "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:
>>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 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
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at uiuc.edu
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