[BioC] Help with Affy TilingArray makePDpackage

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Wed Feb 6 08:10:33 CET 2008 

On Feb 5, 2008, at 8:30 PM, Owen Thomas wrote:

> Hi,
>
> I am trying both the MF and the MR of the version 4 of the yeast
> library file.
>
> I downloaded these from the affymetrix web site:
>
> http://www.affymetrix.com/support/technical/libraryfilesmain.affx
>
> I cannot find the version you are using and would be interested to
> know how you got it.

Ben is using both version 3 and version 4 (as you are), this is  
evident from his text and the filenames.

Kasper


> Thanks for your help,
>
> Regards,
>
> Owen.
>
>
> On 06/02/2008, at 2:58 PM, Ben Bolstad wrote:
>
>> 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_U 
>> S
>> .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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