[BioC] pdInfoBuilder: invalid class object ("ScalarCharacter")
Benilton Carvalho
beniltoncarvalho at gmail.com
Thu Apr 8 12:56:53 CEST 2010
ok... i have just created the packages... they should appear on the
next bioc release. b
On Thu, Apr 8, 2010 at 11:04 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> 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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>>
>
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