[BioC] Help with Affy TilingArray makePDpackage

Owen Thomas owen.thomas at inbox.com
Wed Feb 6 05:30:39 CET 2008 

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.

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_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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