[BioC] pdInfoBuilder: invalid class object ("ScalarCharacter")

Benilton Carvalho beniltoncarvalho at gmail.com
Thu Apr 8 12:10:30 CEST 2010


Aha! I conveniently skipped the 'Gene Titan' part, huh? I'll take a
look at them, thanks, 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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>> >                Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>> >
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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