[BioC] pdInfoBuilder: invalid class object ("ScalarCharacter")
Benilton Carvalho
beniltoncarvalho at gmail.com
Wed Apr 7 23:25:59 CEST 2010
i assume you're aware that this package is available for download via
biocLite()... the updated version, with na30, will be released with
the next bioc. b
On Wed, Apr 7, 2010 at 10:17 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Thanks Vince, that did the trick.
> Working fine now.
> Guido
>
>
> ________________________________
>
> From: Vincent Carey [mailto:stvjc at channing.harvard.edu]
> Sent: 07 April 2010 21:48
> To: Hooiveld, Guido
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] pdInfoBuilder: invalid class object
> ("ScalarCharacter")
>
>
> This is not a message about a file format. It says that the
> input to the class definition for slot transFile is of the wrong class.
> Try
>
> transFile = new("ScalarCharacter", [your filename])
>
> and see where you get. Note
>
> > getClass("AffyGenePDInfoPkgSeed")
> Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"]
>
> Slots:
>
>
> Name: pgfFile clfFile probeFile
> transFile
> Class: ScalarCharacter ScalarCharacter ScalarCharacter
> ScalarCharacter
>
>
> Name: coreMps fullMps extendedMps
> geneArray
> Class: ScalarCharacter ScalarCharacter ScalarCharacter
> logical
>
>
> Name: version license author
> email
> Class: character character character
> character
>
>
> Name: biocViews chipName manufacturer
> url
> Class: character character character
> character
>
> Name: genomebuild organism species
> Class: character character character
>
> Extends:
> Class "AffySTPDInfoPkgSeed", directly
> Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed",
> distance 2
> Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance
> 3
>
> showing that some of the slots need to be instances of
> ScalarCharacter, others can be plain character. Furthermore
>
> > getClass("ScalarCharacter")
> Class "ScalarCharacter" [package "Biobase"]
>
> Slots:
>
> Name: .Data
> Class: character
>
> Extends:
> Class "ScalarObject", directly
> Class "character", from data part
> Class "vector", by class "character", distance 2
> Class "data.frameRowLabels", by class "character", distance 2
> Class "characterORMIAME", by class "character", distance 2
>
> note furthermore
>
> > getValidity(getClass("ScalarObject"))
> function (object)
> {
> if (length(object) != 1L)
> paste(class(object), "must have length one")
> else TRUE
> }
> <environment: namespace:Biobase>
>
>
>
>
>
> On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido
> <Guido.Hooiveld at wur.nl> wrote:
>
>
> Dear list,
> I am trying to build an annotation package for the Mouse
> Gene 1.1 ST
> Array Plate (GeneTitan peg array) using pdInfoBuilder.
> As input i use
> the PGF, CLF, etc files downloaded from Affymetrix.
> However, the
> following lines of code do not work; specifically I am
> puzzled by the
> error message that a file is in the wrong "format". Can
> someone please
> explain what this error means (i have never heard of
> 'ScalarCharacter'),
> and how to solve it?
> Thanks,
> Guido
>
>
> http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode=3
> 4000&navAction=jump&aId=productsNav#1_3
> <http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode=
> 3%0A4000&navAction=jump&aId=productsNav#1_3>
>
>
> > library("pdInfoBuilder")
> Loading required package: Biobase
>
> 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: RSQLite
> Loading required package: DBI
> Loading required package: affxparser
> Loading required package: oligo
> Loading required package: oligoClasses
> Loading required package: preprocessCore
> Welcome to oligo version 1.10.0
> >
> > pgfFile = "MoGene-1_1-st-v1.r4.pgf";
> > clfFile = "MoGene-1_1-st-v1.r4.clf";
> > probeFile = "MoGene-1_1-st-v1.mm8.probe.tab";
> > transFile =
> "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv";
> > pkg <- new("AffyGenePDInfoPkgSeed",
> + version="0.0.1",
> + author="Guido Hooiveld",
> email=guido.hooiveld at xxx,
> + biocViews="AnnotationData",
> + genomebuild="mm8",
> + pgfFile=pgfFile, clfFile=clfFile,
> + probeFile=probeFile, transFile=transFile);
> Error in validObject(.Object) :
> invalid class "AffyGenePDInfoPkgSeed" object: invalid
> object for slot
> "transFile"
> in class "AffyGenePDInfoPkgSeed": got class "character",
> should be or extend class "ScalarCharacter"
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] stats graphics grDevices utils datasets
> methods base
>
>
> other attached packages:
> [1] pdInfoBuilder_1.10.1 oligo_1.10.0
> preprocessCore_1.8.0
> [4] oligoClasses_1.8.0 affxparser_1.18.0
> RSQLite_0.8-0
> [7] DBI_0.2-5 Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 Biostrings_2.14.10 IRanges_1.4.9
> splines_2.10.1
> [5] tools_2.10.1
>
>
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet: http://nutrigene.4t.com
> <http://nutrigene.4t.com/>
> email: guido.hooiveld at wur.nl
>
>
>
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>
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