[BioC] PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays

Mary Putt mputt at mail.med.upenn.edu
Tue Nov 4 16:01:51 CET 2008


I have been trying to follow earlier posts as to how to make a package 
that I could use in oligo to read in an Affy expression dataset from the 
HuGene platform. I downloaded what appear to be the correct files from 
the Affy website and tried to run the  makePdInfoPackage(pkg, 
destDir=".") function but received an error as shown below.

Also I was not able to find much documentation on how to build this 
specific package in pdInfoBuilder--are there other sources of 
documentation that I've missed?

Thank you,


R version 2.6.0 (2007-10-03)

 > library("pdInfoBuilder")
Loading required package: Biobase
Loading required package: tools

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: splines
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: oligoClasses
oligo Package - Series 1.5.x
 > library("makePlatformDesign")
Loading required package: affyio
 > list.files()
 [1] "HuGene-1_0-st-v1.AFFX_README.Sequence-Files.txt"        
 [2] "HuGene-1_0-st-v1.exon_analysis_configuration"           
 [3] "HuGene-1_0-st-v1.na26.AFFX_README.NetAffx-CSV-Files.txt"
 [4] "HuGene-1_0-st-v1.na26.hg18.transcript.csv"              
 [5] "HuGene-1_0-st-v1.probe.tab"                             
 [6] "HuGene-1_0-st-v1.r3.bgp"                                
 [7] "HuGene-1_0-st-v1.r3.clf"                                
 [8] "HuGene-1_0-st-v1.r3.mps"                                
 [9] "HuGene-1_0-st-v1.r3.pgf"                                
[10] "HuGene-1_0-st-v1.r3.qcc"                                
[11] "HuGene-1_0-st-v1.r3.README.txt"                         
[12] "HuGene-1_0-st-v1.r3.transcript-probesets.ps"            
[13] "Hugene.mps"                                             
[14] "mk.hugene.pdf.r"                                        
 > tmp<-list.files()
 > #downloaded files from Affy website for hugene array
 > pgfFile<-tmp[9]
 > clfFile<-tmp[7]
 > probeFile<-tmp[5]
 > transFile<-tmp[4]
 > pgfFile
[1] "HuGene-1_0-st-v1.r3.pgf"
 > clfFile
[1] "HuGene-1_0-st-v1.r3.clf"
 > probeFile
[1] "HuGene-1_0-st-v1.probe.tab"
 > transFile
[1] "HuGene-1_0-st-v1.na26.hg18.transcript.csv"
 > pkg<-new("AffyGenePDInfoPkgSeed", version="0.1.0", author="Mary 
Putt", email="mputt at mail.med.upenn.edu", biocViews="AnnotationData", 
genomebuild="UPenn Nov 2008", clfFile=clfFile, pgfFile=pgfFile, 
probeFile=probeFile, transFile=transFile)
 > makePdInfoPackage(pkg, destDir=".")
Creating package in ./pd.hugene.1.0.st.v1
Error in if (isdir[k]) { : missing value where TRUE/FALSE needed
Calls: makePdInfoPackage ... makePdInfoPackage -> createPackage -> 
copySubstitute -> cpSubs
In addition: Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
Execution halted

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