[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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