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@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@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@wur.nl
>
>
>
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>
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