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

[Hooiveld, Guido]

Hi Seth,
No, that is not the case.
I noticed the missing quotes as well after sending the email, but that
happened when I removed part of my email address (b/o spam). Thus, to
confirm, these lines of code do not work:
Guido

> pkg <- new("AffyGenePDInfoPkgSeed",
+           version="0.0.1",
+           author="Guido Hooiveld", email="guido.hooiveld at xxx.nl",
+           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"
> 

 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Seth Falcon
> Sent: 07 April 2010 21:09
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] pdInfoBuilder: invalid class object 
> ("ScalarCharacter")
> 
> 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?
> 
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