[BioC] problem with duplicateCorrelation and ExpressionSet objects

[Gordon K Smyth]

Hi Jenny,

Your example may be reproducible by you, but it's not runnable by me because I don't have you
data.  As I said in my previous email, you need to construct an example which can be run by
someone else.  This means that you need to do one of the following: use public data, or generate
data, or provide data.

As I demonstrated in my previous email, I've already run an example closely analogous to yours and
found no problem.  So analogy is not good enough, we need to run your exact code.

If RWinEdt isn't needed for the example, please don't include it.  I cannot help you with any
session which includes RWinEdt.

By the way, the lattice and Matrix packages have version numbers less than 1.0, meaning that their
authors do not yet consider them to be fully reliable.  Bioconductor packages are not included in
the release if they are still at this stage.

Best wishes
Gordon

On Wed, May 30, 2007 2:58 am, 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
>
> 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