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

[Seth Falcon]

On 4/7/10 11:55 AM, Hooiveld, Guido 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
>
>
>> 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,

Perhaps it is that you are missing quotes around your email address?