[BioC] problem with duplicateCorrelation and ExpressionSet objects
Gordon Smyth
smyth at wehi.EDU.AU
Fri May 25 00:10:16 CEST 2007
Dear Jenny,
I am unable to reproduce your error, despite installing and loading
all the same packages that you have loaded in your session (except
for RWinEdt which I am unable to install in R 2.5.0). For me to help
you further, you would need to provide a reproducible example of the
problem. That is, you need to provide an example of code which can be
run by someone other than yourself which produces the same error.
I give below a complete R session which I have just run, showing that
duplicateCorrelation works fine for me. I have limma 2.11.4 loaded,
but that is the same as 2.10.4.
Best wishes
Gordon
=== R session starts ==========
> library(bovineprobe)
Loading required package: matchprobes
Loading required package: 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)'.
Loading required package: affy
Loading required package: affyio
> library(bovinecdf)
> library(affyQCReport)
Loading required package: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: xtable
Loading required package: affyPLM
Loading required package: affydata
Loading required package: gcrma
Loading required package: RColorBrewer
Loading required package: geneplotter
Loading required package: annotate
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
> library(geneplotter)
> library(RColorBrewer)
> library(simpleaffy)
> library(made4)
Loading required package: ade4
Loading required package: scatterplot3d
> library(scatterplot3d)
> library(ade4)
> library(affyPLM)
> library(affydata)
> library(affycoretools)
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO
Loading required package: RBGL
Loading required package: Category
Loading required package: KEGG
Loading required package: Matrix
Loading required package: biomaRt
Loading required package: XML
Attaching package: 'XML'
The following object(s) are masked from package:graph :
addNode
Loading required package: RCurl
Attaching package: 'biomaRt'
The following object(s) are masked from package:annotate :
getGO
Loading required package: annaffy
> library(annaffy)
> library(xtable)
> library(gcrma)
> library(matchprobes)
> library(biomaRt)
> library(RCurl)
> library(XML)
> library(GOstats)
> library(Category)
> library(lattice)
> library(genefilter)
> library(survival)
> library(KEGG)
> library(RBGL)
> library(annotate)
> library(GO)
> library(graph)
> library(limma)
> library(affy)
> library(affyio)
> library(Biobase)
>
> setwd("changed for confidentiality")
> library(limma)
> targets <- readTargets()
> library(affy)
> x <- ReadAffy(filenames=targets$FileName)
> y <- gcrma(x)
Attaching package: 'mouse4302cdf'
The following object(s) are masked from package:bovinecdf :
i2xy,
xy2i
Adjusting for optical effect..........Done.
Computing affinities.Done.
Adjusting for non-specific binding..........Done.
Normalizing
Calculating Expression
> design <- model.matrix(~factor(targets$CellType))
> corfit <-
duplicateCorrelation(y,design,ndups=1,block=c(1,1,1,2,2,2,2,2,2,2))
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] "splines" "tools" "stats" "graphics" "grDevices"
"utils" "datasets" "methods" "base"
other attached packages:
statmod
mouse4302probe mouse4302cdf affycoretools annaffy
biomaRt RCurl XML
"1.3.0" "1.16.0" "1.16.0" "1.8.0"
"1.8.1" "1.10.0" "0.8-0" "1.7-1"
GOstats Category Matrix KEGG
RBGL GO graph limma
"2.2.3" "2.2.3" "0.99875-1" "1.16.0"
"1.12.0" "1.16.0" "1.14.1" "2.11.4"
made4 scatterplot3d ade4 affyQCReport
geneplotter lattice annotate RColorBrewer
"1.10.0" "0.3-24" "1.4-3" "1.14.0"
"1.14.0" "0.15-5" "1.14.1" "0.2-3"
affyPLM gcrma affydata xtable
simpleaffy genefilter survival bovinecdf
"1.12.0" "2.8.1" "1.11.2" "1.4-6"
"2.10.11" "1.14.1" "2.31" "1.16.0"
bovineprobe matchprobes affy affyio Biobase
"1.16.0" "1.8.1" "1.14.0" "1.4.0" "1.14.0"
============= R session ends ===============
At 01:52 AM 25/05/2007, Jenny Drnevich wrote:
>Hi Gordon,
>
>I'm still having the problem with duplicateCorrelation on an
>ExpressionSet object, even though I upgraded to limma 2.10.4.
>Additionally, the 'fix' of not having the Matrix package loaded
>doesn't work either, unless there's a difference between never
>having loaded the package and detaching the package... Am I doing
>something wrong?
>
>Thanks,
>Jenny
>
> > gcrma.no1 <- gcrma(raw[,-1])
>
> > detach(package:Matrix)
>
> > corfit <-
> duplicateCorrelation(gcrma.no1,design.no1,ndups=1,block=targets$pair[-1])
>Error in as.vector(x, mode) : cannot coerce to vector
>
> > 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:
> bovineprobe bovinecdf affyQCReport geneplotter RColorBrewer
> "1.16.0" "1.16.0" "1.14.0" "1.14.0" "0.2-3"
> simpleaffy made4 scatterplot3d ade4 affyPLM
> "2.10.11" "1.10.0" "0.3-24" "1.4-3" "1.12.0"
> affydata affycoretools annaffy xtable gcrma
> "1.11.2" "1.8.0" "1.8.1" "1.4-3" "2.8.1"
> matchprobes biomaRt RCurl XML GOstats
> "1.8.1" "1.10.0" "0.8-0" "1.7-1" "2.2.3"
> Category lattice genefilter survival KEGG
> "2.2.3" "0.15-4" "1.14.1" "2.31" "1.16.0"
> RBGL annotate GO graph limma
> "1.12.0" "1.14.1" "1.16.0" "1.14.1" "2.10.4"
> affy affyio Biobase RWinEdt
> "1.14.1" "1.4.0" "1.14.0" "1.7-5"
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