[BioC] error when using pdInfoBuilder

[Paul Sanfilippo [guest]]

Hi,

This is my first attempt at analysing some expression data and I'm having trouble trying to create an annotation package using pdInfoBuilder for some rat array data. I've downloaded the appropriate library files from the affymetrix website, but encounter the following error (which I am unsure how to fix):

Thanks for any suggestions.

Regards,

Paul



> seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf,probeFile = probe, transFile = trans, coreMps = core)
> 
> makePdInfoPackage(seed, destDir = ".")
==========================================================================================================================================================
Building annotation package for Affymetrix Gene ST Array
PGF.........: RaGene-2_1-st.pgf
CLF.........: RaGene-2_1-st.clf
Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
Core MPS....: RaGene-2_1-st.mps
==========================================================================================================================================================
Parsing file: RaGene-2_1-st.pgf... OK
Parsing file: RaGene-2_1-st.clf... OK
Creating initial table for probes... Error in .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]) : 
  NA/NaN argument

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] pdInfoBuilder_1.24.0 oligo_1.24.0         oligoClasses_1.22.0  affxparser_1.32.0    RSQLite_0.11.3       DBI_0.2-7            Biobase_2.20.0      
[8] BiocGenerics_0.6.0  

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         BiocInstaller_1.10.1  Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8       ff_2.2-11            
 [7] foreach_1.4.0         GenomicRanges_1.12.4  IRanges_1.18.1        iterators_1.0.6       preprocessCore_1.22.0 splines_3.0.0        
[13] stats4_3.0.0          tools_3.0.0           zlibbioc_1.6.0       

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