[BioC] problem with duplicateCorrelation and ExpressionSet objects
Jenny Drnevich
drnevich at uiuc.edu
Tue May 29 18:58:26 CEST 2007
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
R version 2.5.0 (2007-04-23)
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> library(RWinEdt)
> library(gcrma)
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
Loading required package: matchprobes
Loading required package: splines
> library(limma)
>
> setwd("C:/statistics/Sergio")
>
> raw <- ReadAffy(celfile.path="C:/statistics/Sergio/CELfiles2nd")
> raw
AffyBatch object
size of arrays=732x732 features (9 kb)
cdf=Bovine (24128 affyids)
number of samples=14
number of genes=24128
annotation=bovine
notes=
> gcrma.all <- gcrma(raw)
Adjusting for optical effect..............Done.
Computing affinities.Done.
Adjusting for non-specific binding..............Done.
Normalizing
Calculating Expression
>
> targets <- readTargets("targets2.txt")
>
> temp <- as.numeric(factor(targets$trt))
> temp[temp==2] <- 0
> design.all <- cbind(int=1,HydVnorm=temp)
>
> corfit <-
duplicateCorrelation(gcrma.all,design.all,ndups=1,block=targets$pair)
Loading required package: statmod
> library(Matrix)
Loading required package: lattice
>
> corfit <-
duplicateCorrelation(gcrma.all,design.all,ndups=1,block=targets$pair)
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:
Matrix lattice statmod bovineprobe bovinecdf limma
"0.9975-11" "0.15-4" "1.3.0" "1.16.0" "1.16.0" "2.10.4"
gcrma matchprobes affy affyio Biobase RWinEdt
"2.8.1" "1.8.1" "1.14.1" "1.4.0" "1.14.0" "1.7-5"
>
At 05:10 PM 5/24/2007, Gordon Smyth wrote:
>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"
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
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