[BioC] xps problem with root files

[Benilton Carvalho]

Juan, I can't help you with your request about xps. Very soon you'll
get the proper reply. However, for the record, oligo does handle
HuGene 1.1 as well...
benilton

On 2 October 2012 18:00, Juan Fernández Tajes <jfernandezt at udc.es> 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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