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>... Importing </users> 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> 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>... Importing </users> as <hugene-1_0-st-v1.cxy>... <1102500> records imported...Finished New dataset <hugene-1_0-st-v1> is added to Content... Importing </users> 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@udc.es ---------------------------------------------------------------- [[alternative HTML version deleted]]

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 Fern?ndez 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>... > Importing </users> 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> 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>... > Importing </users> as <hugene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > New dataset <hugene-1_0-st-v1> is added to Content... > Importing </users> 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 Biolog?a Celular y Molecular > Facultad de Ciencias-Universidade da Coru?a > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt at udc.es > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 Fern?ndez 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>... > Importing </users> 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> 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>... > Importing </users> as <hugene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > New dataset <hugene-1_0-st-v1> is added to Content... > Importing </users> 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 Biolog??a Celular y Molecular > Facultad de Ciencias-Universidade da Coru??a > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt at udc.es > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

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=""> escribi?: > >> 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 Fern?ndez 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>... >>> Importing </users> 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> 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>... >>> Importing </users> as <hugene-1_0-st-v1.cxy>... >>> <1102500> records imported...Finished >>> New dataset <hugene-1_0-st-v1> is added to Content... >>> Importing </users> 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 Biolog??a Celular y Molecular >>> Facultad de Ciencias-Universidade da Coru??a >>> Tlf. +34 981 167000 ext 2030 >>> e-mail: jfernandezt at udc.es >>> ---------------------------------------------------------------- >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >