
Sorry about that. I am including the sessionInfo here:

 

> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS", "2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen", type="expression", genomebuild = "mm8")
nimblegen expression 
The package will be called pd.2006.07.18.mm8.refseq.promoter 
Reading 2006-07-18_MM8_RefSeq_promoter.ndf 
Assuming a simple design (NOT multiple-wells).
Correcting probe positions... Done.
Error in getClass(Class, where = topenv(parent.frame())) : 
  "platformDesign" is not a defined class

> sessionInfo() 
R version 2.10.0 beta (2009-10-16 r50118) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] makePlatformDesign_1.10.0 affyio_1.13.5             biomaRt_2.2.0             Ringo_1.10.0              Matrix_0.999375-37        lattice_0.18-3           
 [7] limma_3.2.1               RColorBrewer_1.0-2        pdInfoBuilder_1.10.1      oligo_1.10.2              preprocessCore_1.7.9      oligoClasses_1.7.16      
[13] affxparser_1.18.0         RSQLite_0.8-3             DBI_0.2-5                 Biobase_2.5.8            

loaded via a namespace (and not attached):
 [1] annotate_1.23.4      AnnotationDbi_1.7.20 Biostrings_2.14.12   genefilter_1.25.10   IRanges_1.4.11       RCurl_1.3-1          splines_2.10.0       survival_2.35-8     
 [9] tools_2.10.0         XML_2.6-0            xtable_1.5-6        
> 
 
> Date: Mon, 1 Mar 2010 15:38:18 -0500
> Subject: Re: [BioC] makePDpackage
> From: seandavi@gmail.com
> To: genome1976@hotmail.com
> CC: bioconductor@stat.math.ethz.ch
> 
> On Mon, Mar 1, 2010 at 3:27 PM, somnath bandyopadhyay
> <genome1976@hotmail.com> wrote:
> >
> > Hi,
> >
> > I am trying to annotate the Nimblegen 385k mm8  refseq promoter chip and the following is what I have been using:
> >
> >
> >
> >> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS", "2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen", type="expression", genomebuild = "mm8")
> > nimblegen expression
> > The package will be called pd.2006.07.18.mm8.refseq.promoter
> > Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> > Assuming a simple design (NOT multiple-wells).
> > Correcting probe positions... Done.
> > Error in getClass(Class, where = topenv(parent.frame())) :
> >  "platformDesign" is not a defined class
> >
> >
> >
> > Could anybody help me out with this? Moreover, is there a way to convert .pair files into .XYS files for nimblegen?
> 
> Hi, Somnath. It is always useful to include sessionInfo() output when
> reporting errors. Without this information, it is difficult to
> determine what the problem might be.
> 
> Sean
 		 	   		  
_________________________________________________________________
Hotmail: Trusted email with Microsoft’s powerful SPAM protection.

	[[alternative HTML version deleted]]

