[BioC] xps problem with root files

[cstrato]

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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