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

Mary Putt mputt at mail.med.upenn.edu
Tue Nov 11 21:22:36 CET 2008


Sean/Benilton,

Thanks for all your help--I think we finally got it. Installing a new 
package in Windows seemed not in my near future so I waited for an 
updated R 2.8 and Bioconductor and then proceeded. Here is my code 
summarized from the various email for doing this in case anyone else 
needs it.

Thank you both very much!


Mary



library("pdInfoBuilder")
library("makePlatformDesign")

list.files()
tmp<-list.files()
#downloaded files from Affy website for hugene array

pgfFile<-tmp[9]
clfFile<-tmp[7]
probeFile<-tmp[5]
transFile<-tmp[4]

pgfFile
clfFile
probeFile
transFile

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=".")

##########
#now install package from the new directory using
#R CMD INSTALL pkg on Linux
#once package installed proceed with the following to get
#the rma-normalized data
#################

library("pd.hugene.1.0.st.v1")
library("oligo")

dat<-read.celfiles(filenames=list.celfiles())
eset<-rma(dat)
exprs.eset<-exprs(eset)


Sean Davis wrote:
>
>
> On Tue, Nov 4, 2008 at 9:15 PM, Mary Putt <mputt at mail.med.upenn.edu 
> <mailto:mputt at mail.med.upenn.edu>> wrote:
>
>     Yes you're right but I'm stumped about how to do this for a
>     self-made package? There is install.packge() and install from a
>     local zip but otherwise I'm stumped? 
>
>
> Are you on Windows?  If so, you will need the RTools--see the 
> R-for-Windows FAQ.  If not, then you can, at the command line, type:
>
> R CMD INSTALL directory
>
> where directory is the directory of the package. 
>
> Sean
>
>  
>
>
>
>     Sean Davis wrote:
>
>
>
>         On Tue, Nov 4, 2008 at 5:10 PM, Mary Putt
>         <mputt at mail.med.upenn.edu <mailto:mputt at mail.med.upenn.edu>
>         <mailto:mputt at mail.med.upenn.edu
>         <mailto:mputt at mail.med.upenn.edu>>> wrote:
>
>            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?
>
>
>         This error typically arises from copying a library into a
>         library directory without actually installing it.  You need to
>         install the package before calling library().
>
>         Sean
>
>          
>
>            R version 2.8.0 (2008-10-20)
>            Copyright (C) 2008 The R Foundation for Statistical Computing
>            ISBN 3-900051-07-0
>
>            R is free software and comes with ABSOLUTELY NO WARRANTY.
>            You are welcome to redistribute it under certain conditions.
>            Type 'license()' or 'licence()' for distribution details.
>
>             Natural language support but running in an English locale
>
>            R is a collaborative project with many contributors.
>            Type 'contributors()' for more information and
>            'citation()' on how to cite R or R packages in publications.
>
>            Type 'demo()' for some demos, 'help()' for on-line help, or
>            'help.start()' for an HTML browser interface to help.
>            Type 'q()' to quit R.
>
>            [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
>         <http://HuGene-1_0-st-v1.r3.transcript-probesets.ps>
>            <http://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
>         <mailto:mputt at mail.med.upenn.edu>
>            <mailto:mputt at mail.med.upenn.edu
>         <mailto: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 <http://is.na> <http://is.na>(x) : is.na
>         <http://is.na> <http://is.na>() applied to
>
>            non-(list or vector) of type 'NULL'
>            2: In is.na <http://is.na> <http://is.na>(x) : is.na
>         <http://is.na> <http://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
>         <http://HuGene-1_0-st-v1.r3.transcript-probesets.ps>
>                    <http://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
>         <mailto:mputt at mail.med.upenn.edu>
>                    <mailto:mputt at mail.med.upenn.edu
>         <mailto: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 <http://is.na> <http://is.na>(x) : is.na
>         <http://is.na> <http://is.na>()
>
>                    applied to non-(list or vector) of type 'NULL'
>                    Execution halted
>
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