[BioC] Help with Affy TilingArray makePDpackage
Ben Bolstad
bmb at bmbolstad.com
Wed Feb 6 04:58:26 CET 2008
At least on my machine the version 3 of this file parses fine:
> library(affyio)
> bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v03.bpmap")
> sessionInfo()
R version 2.7.0 Under development (unstable) (2008-02-02 r44303)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] affyio_1.7.9
> names(bpmap)
[1] "Header" "SequenceDescription" "SeqHead.PosInfo"
> bpmap$Header
$magic.number
[1] "PHT7\r\n\032\n"
$version
[1] 2
$n.seq
[1] 87
>
Digging around for the v4 of this file (again no problem)
> bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v04.bpmap")
> bpmap$Header
$magic.number
[1] "PHT7\r\n\032\n螑"
$version
[1] 2
$n.seq
[1] 87
On Tue, 2008-02-05 at 22:50 -0500, Benilton Carvalho wrote:
> Unless you have other reasons to use R-2.7.0, don't do that... It'll
> automatically download devel versions of BioConductor packages, and
> it's hard to guarantee that they will be stable enough....
>
> I'd need to find the BPMAP you're working with, so debugging will
> simplified... is it at affy's website? where exactly?
>
> thanks,
>
> b
>
>
>
> On Feb 5, 2008, at 10:32 PM, Owen Thomas wrote:
>
> > I downloaded the affyio 1.7.10 source and installed, but I still
> > have exactly the same error, which occurs in the
> > ReadBPMAPFileIntoRList c function:
> >
> > bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v04.bpmap")
> > Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> >
> > It seems that the Mac OS X binary of affyio 1.7.1 is compiled
> > against a development version of R, would you recommend upgrading my
> > version of R?
> >
> > Anyway, to confirm the installation my sessionInfo is
> >
> > > sessionInfo ()
> > R version 2.6.1 (2007-11-26)
> > powerpc-apple-darwin8.10.1
> >
> > locale:
> > C
> >
> > attached base packages:
> > [1] splines tools stats graphics grDevices utils
> > datasets
> > [8] methods base
> >
> > other attached packages:
> > [1] makePlatformDesign_1.2.0 oligo_1.2.2
> > oligoClasses_1.0.3
> > [4] affxparser_1.10.2 AnnotationDbi_1.0.6
> > preprocessCore_1.0.0
> > [7] RSQLite_0.6-4 DBI_0.2-4 Biobase_1.16.2
> > [10] affyio_1.7.10
> >
> > loaded via a namespace (and not attached):
> > [1] rcompgen_0.1-17
> >
> >
> > Regards,
> >
> > Owen.
> >
> >
> > On 06/02/2008, at 2:03 PM, Benilton Carvalho wrote:
> >
> >> Do you want to try a non-recommended approach?
> >>
> >> Install the devel version of affyio, I recall Ben fixing something
> >> like this not long ago:
> >>
> >> http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html
> >>
> >> Please let us know how it goes...
> >>
> >> b
> >>
> >> On Feb 5, 2008, at 9:43 PM, Owen Thomas wrote:
> >>
> >>> Hi,
> >>>
> >>> I am running affyio 1.6.1,
> >>>
> >>> as confirmed by the sessionInfo:
> >>>
> >>> > sessionInfo ()
> >>> R version 2.6.1 (2007-11-26)
> >>> powerpc-apple-darwin8.10.1
> >>>
> >>> locale:
> >>> C
> >>>
> >>> attached base packages:
> >>> [1] splines tools stats graphics grDevices utils
> >>> datasets
> >>> [8] methods base
> >>>
> >>> other attached packages:
> >>> [1] makePlatformDesign_1.2.0 oligo_1.2.2
> >>> oligoClasses_1.0.3
> >>> [4] affxparser_1.10.2 AnnotationDbi_1.0.6
> >>> preprocessCore_1.0.0
> >>> [7] RSQLite_0.6-4 DBI_0.2-4 Biobase_1.16.2
> >>> [10] affyio_1.6.1
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] rcompgen_0.1-17
> >>>
> >>>
> >>> Thanks,
> >>>
> >>> Owen.
> >>>
> >>> On 06/02/2008, at 1:30 PM, Benilton Carvalho wrote:
> >>>
> >>>> You didn't provide the results of your sessionInfo()
> >>>>
> >>>> But the error is given by affyio, suggesting that you're running
> >>>> an outdated version (the latest of affyio is 1.6.1).
> >>>>
> >>>> Please, ensure you're running this version and let us know what
> >>>> your sessionInfo() is.
> >>>>
> >>>> best,
> >>>> b
> >>>>
> >>>>
> >>>> On Feb 5, 2008, at 9:11 PM, Owen Thomas wrote:
> >>>>
> >>>>> Hi,
> >>>>>
> >>>>> I am having trouble using the makePDpackage function, other people
> >>>>> have had the same problem:
> >>>>>
> >>>>> https://stat.ethz.ch/pipermail/bioconductor/2008-January/020922.html
> >>>>>
> >>>>> I have found no solution though, if anyone could help me
> >>>>> understand
> >>>>> what's going on I would greatly appreciate it.
> >>>>>
> >>>>> The concise problem is:
> >>>>>
> >>>>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif",
> >>>>> manufacturer="affymetrix", type="tiling")
> >>>>> affymetrix tiling
> >>>>>
> >>>>> The package will be called pd.sc03b.mf.v04
> >>>>>
> >>>>> Error in makeBPMAPenv(designFile, file1, genomebuild =
> >>>>> genomebuild) :
> >>>>> SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Owen.
> >>>>>
> >>>>> Full R session:
> >>>>>
> >>>>> R version 2.6.1 (2007-11-26)
> >>>>> Copyright (C) 2007 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.
> >>>>>
> >>>>>> library (makePlatformDesign)
> >>>>> Loading required package: affyio
> >>>>> Loading required package: oligo
> >>>>> 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: splines
> >>>>> Loading required package: RSQLite
> >>>>> Loading required package: DBI
> >>>>> Loading required package: preprocessCore
> >>>>> Loading required package: AnnotationDbi
> >>>>> Loading required package: affxparser
> >>>>> Loading required package: oligoClasses
> >>>>> This is the oligo package
> >>>>>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif",
> >>>>> manufacturer="affymetrix", type="tiling")
> >>>>> affymetrix tiling
> >>>>> The package will be called pd.sc03b.mf.v04
> >>>>> Error in makeBPMAPenv(designFile, file1, genomebuild =
> >>>>> genomebuild) :
> >>>>> SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> >>>>>> traceback ()
> >>>>> 3: .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")
> >>>>> 2: makeBPMAPenv(designFile, file1, genomebuild = genomebuild)
> >>>>> 1: makePDpackage("Sc03b_MF_v04.bpmap", file1 = "Sc03b_MF_v04.cif",
> >>>>> manufacturer = "affymetrix", type = "tiling")
> >>>>>
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> >>>>
> >>>
> >>
> >
>
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