[BioC] pdInfoBuilder: invalid class object ("ScalarCharacter")
Hooiveld, Guido
Guido.Hooiveld at wur.nl
Thu Apr 8 12:04:07 CEST 2010
Hi Benilton,
Thanks for your suggestion. However, I did check before both release and dev annotation packages, but I could not found a pd package for this specific array.
I assume you refer to pd.mogene.1.0.st.v1,
http://www.bioconductor.org/packages/devel/data/annotation/html/pd.mogene.1.0.st.v1.html
which is for the cardridge mouse Gene ST array (=version 1.0) [MoGene-1_0-st-v1],
whereas I do have data generated on the peg (plate, GeneTitan) version of this array (= mouse Gene ST array version 1.1) [MoGene-1_1-st-v1].
Guido
> -----Original Message-----
> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com]
> Sent: 07 April 2010 23:26
> To: Hooiveld, Guido
> Cc: Vincent Carey; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] pdInfoBuilder: invalid class object
> ("ScalarCharacter")
>
> 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&navMod
> > e= 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
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> >
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
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