[BioC] xps problem with root files

[cstrato]

Dear Juan,

I am glad to hear that the problem is solved.

Best regards,
Christian


On 10/2/12 11:02 PM, Juan Fernandez Tajes wrote:
> Dear Christian,
>
> Creating my own "schemes" directory worked fine,
>
> Many thanks
>
> Juan
>
> El 02/10/2012, a las 22:19, cstrato <cstrato at aon.at> escribió:
>
>> Dear Juan,
>>
>> You have used:
>> scheme.hugene11stv1 <- root.scheme(file.path(.path.package("xps"), "schemes", "hugene11stv1.root"))
>>
>> Did you start a new R session after moving the root scheme files to the schemes directory in package xps?
>>
>> BTW, I would not recommend to move the scheme files to the directories of package xps. I would suggest that you create your own 'schemes' directory and move all root scheme files to this directory. Could you try this option, too?
>>
>> Please let me know if you could solve the problem.
>>
>> Best regards,
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>>
>> On 10/2/12 7:00 PM, Juan Fernández Tajes wrote:
>>> Dear list,
>>>
>>> I´ve already analysed microarray data from Hugene11 st with oligo package. However I would like to use xps package as well because I want to compare results from Hugene 1.0 and Hugene 1.1 and I think xps package is the right one.
>>> I have created the root scheme following the script proposed in the package:
>>>
>>> scheme.hugene11stv1.na32 <- import.exon.scheme("hugene11stv1", filedir = file.path(scmdir, "na32"),
>>> + file.path(libdir, "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.clf"),
>>> + file.path(libdir, "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.pgf"),
>>> + file.path(anndir, "Version08Oct", "HuGene-1_1-st-v1.na32.hg19.probeset.csv"),
>>> + file.path(anndir, "Version08Oct", "HuGene-1_1-st-v1.na32.hg19.transcript.csv"))
>>> Creating new file </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/schemes/na32/hugene11stv1.root>...
>>> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/libraryfiles/HuGene-1_1-st-v1_strip_libraryfile/HuGene-1_1-st-v1.r4.clf> as <HuGene-1_1-st-v1.cxy>...
>>> <803480> records imported...Finished
>>> Warning: Number of entries <803480> is not equal to <1178100>.
>>> New dataset <HuGene-1_1-st-v1> is added to Content...
>>> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/Annotation/Version08Oct/HuGene-1_1-st-v1.na32.hg19.probeset.csv> as <HuGene-1_1-st-v1.anp>...
>>> Number of probesets is <257430>.
>>> <33297> records read...Finished
>>> <32919> records imported...Finished
>>> shed
>>>> # HuGene-1_0-st-v1.r4: used as exon array
>>>> scheme.hugene10stv1.na32 <- import.exon.scheme("hugene10stv1", filedir = file.path(scmdir, "na32"),
>>> + file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.clf"),
>>> + file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.pgf"),
>>> + file.path(anndir, "Version11Jul", "HuGene-1_0-st-v1.na32.hg19.probeset.csv"),
>>> + file.path(anndir, "Version11Jul", "HuGene-1_0-st-v1.na32.hg19.transcript.csv"))
>>> Creating new file </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/schemes/na32/hugene10stv1.root>...
>>> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/libraryfiles/HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.clf> as <HuGene-1_0-st-v1.cxy>...
>>> <1102500> records imported...Finished
>>> New dataset <HuGene-1_0-st-v1> is added to Content...
>>> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/Annotation/Version11Jul/HuGene-1_0-st-v1.na32.hg19.probeset.csv> as <HuGene-1_0-st-v1.anp>...
>>> Number of probesets is <257430>.
>>> <33297> records read...Finished
>>> <32919> records imported...Finished
>>> shed
>>>
>>> After creating both root schemes (for Hugene 1.0 and 1.1 st) I moved them to a schemes directory in xps package
>>>
>>> However, when I try to import the root schemes I obtained the following error:
>>>> scheme.hugene11stv1 <- root.scheme(file.path(.path.package("xps"), "schemes", "hugene11stv1.root"))
>>> Error en validROOTFile(rootfile, "none") :
>>> ‘rootfile’ of class ‘none’ is missing or not a ROOT file *.root
>>>> scheme.hugene10stv1 <- root.scheme(file.path(.path.package("xps"), "schemes", "hugene10stv1.root"))
>>> Error en validROOTFile(rootfile, "none") :
>>> ‘rootfile’ of class ‘none’ is missing or not a ROOT file *.root
>>>
>>>
>>> Any ideas ?
>>>
>>> Juan
>>>
>>> My sessionInfo is the following:
>>> R version 2.15.1 (2012-06-22)
>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>>
>>> locale:
>>> [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] xps_1.16.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.15.1
>>>
>>>
>>>
>>>
>>> ---------------------------------------------------------------
>>> Juan Fernandez Tajes, ph. D
>>> Grupo XENOMAR
>>> Departamento de Biología Celular y Molecular
>>> Facultad de Ciencias-Universidade da Coruña
>>> Tlf. +34 981 167000 ext 2030
>>> e-mail: jfernandezt at udc.es
>>> ----------------------------------------------------------------
>>>
>>>
>>>
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>>>
>>>
>>>
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>
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