[BioC] PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays
Mary Putt
mputt at mail.med.upenn.edu
Tue Nov 4 23:10:26 CET 2008
Benilton,
Thanks for your reply. It occurred to me as well that this might be a
version problem. The original error message was based on a run on a
linux server running R 2.6. Then I updated my PC to R 2.8 and to the
most recent bioconductor.
This time it appeared as if the package was created. However when I
tried to attach the library it failed and gave me the following error.
>library("pd.hugene.1.0.st.v1")
Error in library("pd.hugene.1.0.st.v1") :
'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0?
Thank you,
Mary
R version 2.8.0 (2008-10-20)
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[Previously saved workspace restored]
> getwd()
[1] "L:/Affy/Hugene"
> setwd("L:/Affy/Hugene")
>
> 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" [15]
"mk.hugene.pdf.win.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
loadUnitsByBatch took 119.71 sec
loadAffyCsv took 398.77 sec
loadAffySeqCsv took 221.52 sec
DB sort, index creation took 554.41 sec
[1] TRUE
Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>library("pd.hugene.1.0.st.v1")
Error in library("pd.hugene.1.0.st.v1") :
'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0?
Benilton Carvalho wrote:
> Hello Mary,
>
> can you also provide your sessionInfo()?
>
> I also wonder if it is reproducible on the latest R.
>
> Thank you,
> b
>
> On Nov 4, 2008, at 1:01 PM, Mary Putt wrote:
>
>> Hi,
>>
>> 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,
>>
>> Mary
>>
>>
>> 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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