xps library with mouse gene 1.0 transcript arrays
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 11 days ago
Germany
Hi everybody, I am trying to work with the xps package on mouse transcript arrays but having problem creating the root scheme. This is the command I am using to start with (taken from the scripts given with the package) scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir = file.path(scmdir, "na33"), file.path(libdir, "MoGene1_0_libFiles", "MoGene-1_0-st-v1.r4.clf"), file.path(libdir, "MoGene1_0_libFiles", "MoGene-1_0-st-v1.r4.pgf"), file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.probeset.csv"), file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.transcript.csv")) But when I am running this command I get the following error massage: Creating new file </users> ... Importing </users> as <mogene-1_0-st-v1.cxy>... <1102500> records imported...Finished New dataset <mogene-1_0-st-v1> is added to Content... Importing </users> as <mogene-1_0-st-v1.anp>... Note: The following header columns are missing or in wrong order: <mouse_fl> <mouse_mrna> Number of probesets is <269751>. <269751> records read...Finished <269049> records imported...Finished <215654> exon annotations imported. Importing </users> as <mogene-1_0-st-v1.scm>... Reading data from input file... Number of probesets is <241576>. Note: Number of annotated probesets <269751> is not equal to number of probesets <241576>. <241576> records read...Finished Sorting data for probeset_type and position... Total number of controls is <45> Filling trees with data for probeset type: control->chip... Number of control->chip items is <0>. Filling trees with data for probeset type: control->bgp... Filling trees with data for probeset type: control->affx... Number of control->affx probesets is <21>. *Error: Number of control->affx imported <21> is not equal to number of annotated AFFX controls <167>.* *Error: CDF with version/magic number </users> is not supported.* *Error in import.exon.scheme("mogene10stv1", filedir = file.path(scmdir, : error in function ‘ImportExonSchemes’* I would like to know what I am doing wrong and how to do it right, so that the scheme will be uploaded into R with the right annotation files. Thanks Assa I'm working on MacBook Pro 10.7.5 R session info - > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.16.0 BiocGenerics_0.2.0 xps_1.16.0 [4] BiocInstaller_1.4.9 loaded via a namespace (and not attached): [1] tools_2.15.0 [[alternative HTML version deleted]]
Annotation cdf xps Annotation cdf xps • 1.3k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.1 years ago
Austria
Dear Assa, I assume that you get the error since you are mixing MoGene-1_0-st pgf-files with MoGene-2_0-st annotation files. For MoGene-2_0-st you need to do: scheme.mogene20st.na33 <- import.exon.scheme("mogene20stv1", filedir = file.path(scmdir, "na33"), file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.clf"), file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.pgf"), file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.probeset.csv"), file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.transcript.csv")) For MoGene-1_0-st arrays you would need the MoGene-1_0-st annotation files. Furthermore, your version of xps is pretty old, even for R-2.15.x. I would suggest to update to the latest versions of R and xps. 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 9/23/13 3:02 PM, Assa Yeroslaviz wrote: > Hi everybody, > > I am trying to work with the xps package on mouse transcript arrays but > having problem creating the root scheme. > > This is the command I am using to start with (taken from the scripts > given with the package) > > scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir = > file.path(scmdir, "na33"), > file.path(libdir, "MoGene1_0_libFiles", > "MoGene-1_0-st-v1.r4.clf"), > file.path(libdir, "MoGene1_0_libFiles", > "MoGene-1_0-st-v1.r4.pgf"), > file.path(anndir, > "MoGene-2_0-st-v1.na33.2.mm10.probeset.csv"), > file.path(anndir, > "MoGene-2_0-st-v1.na33.2.mm10.transcript.csv")) > > But when I am running this command I get the following error massage: > Creating new file > </users>... > Importing > </users> > as <mogene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > New dataset <mogene-1_0-st-v1> is added to Content... > Importing > </users> > as <mogene-1_0-st-v1.anp>... > Note: The following header columns are missing or in wrong order: > <mouse_fl> > <mouse_mrna> > Number of probesets is <269751>. > <269751> records read...Finished > <269049> records imported...Finished > <215654> exon annotations imported. > Importing > </users> > as <mogene-1_0-st-v1.scm>... > Reading data from input file... > Number of probesets is <241576>. > Note: Number of annotated probesets <269751> is not equal to number > of probesets <241576>. > <241576> records read...Finished > Sorting data for probeset_type and position... > Total number of controls is <45> > Filling trees with data for probeset type: control->chip... > Number of control->chip items is <0>. > Filling trees with data for probeset type: control->bgp... > Filling trees with data for probeset type: control->affx... > Number of control->affx probesets is <21>. > *Error: Number of control->affx imported <21> is not equal to number of > annotated AFFX controls <167>.* > *Error: CDF with version/magic number > </users> > is not supported.* > *Error in import.exon.scheme("mogene10stv1", filedir = file.path(scmdir, : > error in function ?ImportExonSchemes?* > > I would like to know what I am doing wrong and how to do it right, so > that the scheme will be uploaded into R with the right annotation files. > > Thanks > > Assa > > I'm working on MacBook Pro 10.7.5 > R session info - > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biobase_2.16.0 BiocGenerics_0.2.0 xps_1.16.0 > [4] BiocInstaller_1.4.9 > > loaded via a namespace (and not attached): > [1] tools_2.15.0
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Hi Christian, thanks for the quick response. This is a foolish error and I didn't pay enough attention. Sorry. I took your advice and updated to R 3.0.1. Now I have a different problem (which I think has something to do with root, but I can't interpret it correctly). This is what I do: library(xps) libdir <- "/Users/ayeroslaviz/Documents/Annotations/xps" anndir <- "/Users/ayeroslaviz/Documents/Annotations/xps/MoGene1.0_Annotations" scmdir <- "/Users/ayeroslaviz/Documents/Annotations/xps" #MoGene-1_0-st-v1.r4: used as exon array scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir = file.path(scmdir, "na33"), file.path(libdir, "MoGene1_0_libFiles", "MoGene- 1_0-st-v1.r4.clf"), file.path(libdir, "MoGene1_0_libFiles", "MoGene- 1_0-st-v1.r4.pgf"), file.path(anndir, "MoGene-1_0-st-v1.na33.2.mm9.probeset.csv"), file.path(anndir, "MoGene- 1_0-st-v1.na33.2.mm9.transcript.csv")) and this is what I get as an error: Creating new file </users>. .. Importing </users> as <mogene-1_0-st-v1.cxy>... <1102500> records imported...Finished *** Break *** segmentation violation tr: Illegal byte sequence =========================================================== There was a crash. This is the entire stack trace of all threads: =========================================================== Thread 1 (process 54446): #0 0x00007fff830ec168 in wait4 () #1 0x00007fff8e91a5f5 in system () #2 0x0000000137a0b2f9 in TUnixSystem::StackTrace () #3 0x0000000137a08e54 in TUnixSystem::DispatchSignals () #4 <signal handler="" called=""> #5 0x00000001379d9674 in TClass::GetStreamerInfo () #6 0x0000000138925777 in TBufferFile::WriteClones () #7 0x0000000138923d0a in TBufferFile::WriteObjectClass () #8 0x0000000138923e26 in TBufferFile::WriteObjectAny () #9 0x00000001379c1099 in TList::Streamer () #10 0x0000000138923d0a in TBufferFile::WriteObjectClass () #11 0x0000000138923e26 in TBufferFile::WriteObjectAny () #12 0x0000000138923442 in TBufferFile::WriteFastArray () #13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> () #14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction () #15 0x00000001389260ed in TBufferFile::ApplySequence () #16 0x000000013892601d in TBufferFile::WriteClassBuffer () #17 0x000000013948f180 in TTree::Streamer () #18 0x0000000138960abc in TKey::TKey () #19 0x00000001389367db in TFile::CreateKey () #20 0x000000013892ea7e in TDirectoryFile::WriteTObject () #21 0x000000013795928b in TObject::Write () #22 0x00000001340266bf in XTreeSet::WriteTree () #23 0x000000013405b2cf in XGenomeChip::ImportLayout () #24 0x000000013403c9da in XDNAChip::Import () #25 0x00000001340238fe in XManager::Import () #26 0x000000013406956e in XSchemeManager::NewScheme () #27 0x00000001340f3702 in ImportExonSchemes () #28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, op=0x1313ffb20, args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734 #29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at eval.c:635 #30 0x00000001000a2176 in Rf_DispatchOrEval (call=0x7fff5fbfdc20, op=0x7fff5fbfdc20, generic=0x7fff5fbfdc20 "pܿ_=========================================================== The lines below might hint at the cause of the crash. If they do not help you then please submit a bug report at http://root.cern.ch/bugs. Please post the ENTIRE stack trace from above as an attachment in addition to anything else that might help us fixing this issue. =========================================================== #5 0x00000001379d9674 in TClass::GetStreamerInfo () #6 0x0000000138925777 in TBufferFile::WriteClones () #7 0x0000000138923d0a in TBufferFile::WriteObjectClass () #8 0x0000000138923e26 in TBufferFile::WriteObjectAny () #9 0x00000001379c1099 in TList::Streamer () #10 0x0000000138923d0a in TBufferFile::WriteObjectClass () #11 0x0000000138923e26 in TBufferFile::WriteObjectAny () #12 0x0000000138923442 in TBufferFile::WriteFastArray () #13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> () #14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction () #15 0x00000001389260ed in TBufferFile::ApplySequence () #16 0x000000013892601d in TBufferFile::WriteClassBuffer () #17 0x000000013948f180 in TTree::Streamer () #18 0x0000000138960abc in TKey::TKey () #19 0x00000001389367db in TFile::CreateKey () #20 0x000000013892ea7e in TDirectoryFile::WriteTObject () #21 0x000000013795928b in TObject::Write () #22 0x00000001340266bf in XTreeSet::WriteTree () #23 0x000000013405b2cf in XGenomeChip::ImportLayout () #24 0x000000013403c9da in XDNAChip::Import () #25 0x00000001340238fe in XManager::Import () #26 0x000000013406956e in XSchemeManager::NewScheme () #27 0x00000001340f3702 in ImportExonSchemes () #28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, op=0x1313ffb20, args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734 #29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at eval.c:635 =========================================================== Does anyone has any idea what that means? Do I need to re-install root again? Thanks Assa On Mon, Sep 23, 2013 at 3:46 PM, cstrato <cstrato@aon.at> wrote: > Dear Assa, > > I assume that you get the error since you are mixing MoGene-1_0-st > pgf-files with MoGene-2_0-st annotation files. > > For MoGene-2_0-st you need to do: > > scheme.mogene20st.na33 <- import.exon.scheme("**mogene20stv1", filedir = > file.path(scmdir, "na33"), > file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.clf"), > file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.pgf"), > > file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.**probeset.csv"), > file.path(anndir, "MoGene- 2_0-st-v1.na33.2.mm10.**transcript.csv")) > > For MoGene-1_0-st arrays you would need the MoGene-1_0-st annotation files. > > Furthermore, your version of xps is pretty old, even for R-2.15.x. I would > suggest to update to the latest versions of R and xps. > > 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 9/23/13 3:02 PM, Assa Yeroslaviz wrote: > >> Hi everybody, >> >> I am trying to work with the xps package on mouse transcript arrays but >> having problem creating the root scheme. >> >> This is the command I am using to start with (taken from the scripts >> given with the package) >> >> scheme.mogene10stv1.na33 <- import.exon.scheme("**mogene10stv1", filedir >> = >> file.path(scmdir, "na33"), >> file.path(libdir, "MoGene1_0_libFiles", >> "MoGene-1_0-st-v1.r4.clf"), >> file.path(libdir, "MoGene1_0_libFiles", >> "MoGene-1_0-st-v1.r4.pgf"), >> file.path(anndir, >> "MoGene-2_0-st-v1.na33.2.mm10.**probeset.csv"), >> file.path(anndir, >> "MoGene-2_0-st-v1.na33.2.mm10.**transcript.csv")) >> >> But when I am running this command I get the following error massage: >> Creating new file >> </users>> mogene10stv1.root>... >> Importing >> </users>> libFiles/MoGene-1_0-st-v1.r4.**clf> >> as <mogene-1_0-st-v1.cxy>... >> <1102500> records imported...Finished >> New dataset <mogene-1_0-st-v1> is added to Content... >> Importing >> </users>> Annotations//MoGene-2_0-st-v1.**na33.2.mm10.probeset.csv> >> as <mogene-1_0-st-v1.anp>... >> Note: The following header columns are missing or in wrong order: >> <mouse_fl> >> <mouse_mrna> >> Number of probesets is <269751>. >> <269751> records read...Finished >> <269049> records imported...Finished >> <215654> exon annotations imported. >> Importing >> </users>> libFiles/MoGene-1_0-st-v1.r4.**pgf> >> as <mogene-1_0-st-v1.scm>... >> Reading data from input file... >> Number of probesets is <241576>. >> Note: Number of annotated probesets <269751> is not equal to number >> of probesets <241576>. >> <241576> records read...Finished >> Sorting data for probeset_type and position... >> Total number of controls is <45> >> Filling trees with data for probeset type: control->chip... >> Number of control->chip items is <0>. >> Filling trees with data for probeset type: control->bgp... >> Filling trees with data for probeset type: control->affx... >> Number of control->affx probesets is <21>. >> *Error: Number of control->affx imported <21> is not equal to number of >> annotated AFFX controls <167>.* >> *Error: CDF with version/magic number >> </users>> libFiles/MoGene-1_0-st-v1.r4.**pgf> >> is not supported.* >> *Error in import.exon.scheme("**mogene10stv1", filedir = >> file.path(scmdir, : >> error in function ‘ImportExonSchemes’* >> >> >> I would like to know what I am doing wrong and how to do it right, so >> that the scheme will be uploaded into R with the right annotation files. >> >> Thanks >> >> Assa >> >> I'm working on MacBook Pro 10.7.5 >> R session info - >> > sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] Biobase_2.16.0 BiocGenerics_0.2.0 xps_1.16.0 >> [4] BiocInstaller_1.4.9 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 >> > [[alternative HTML version deleted]]
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Dear Assa, The 'segmentation violation' is a hint that the wrong version of ROOT is used. Downloading the following binary for Mac OS X 10.7.5 will solve the problem: ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz Best regards, Christian On 9/23/13 9:23 PM, Assa Yeroslaviz wrote: > Hi Christian, > > thanks for the quick response. > This is a foolish error and I didn't pay enough attention. Sorry. > > I took your advice and updated to R 3.0.1. > Now I have a different problem (which I think has something to do with > root, but I can't interpret it correctly). > > This is what I do: > library(xps) > libdir <- "/Users/ayeroslaviz/Documents/Annotations/xps" > anndir <- > "/Users/ayeroslaviz/Documents/Annotations/xps/MoGene1.0_Annotations" > scmdir <- "/Users/ayeroslaviz/Documents/Annotations/xps" > #MoGene-1_0-st-v1.r4: used as exon array > > scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir = > file.path(scmdir, "na33"), > file.path(libdir, "MoGene1_0_libFiles", "MoGene- 1_0-st-v1.r4.clf"), > file.path(libdir, "MoGene1_0_libFiles", "MoGene- 1_0-st-v1.r4.pgf"), > file.path(anndir, "MoGene- 1_0-st-v1.na33.2.mm9.probeset.csv"), > file.path(anndir, "MoGene- 1_0-st-v1.na33.2.mm9.transcript.csv")) > > and this is what I get as an error: > Creating new file > </users>... > Importing > </users> > as <mogene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > > *** Break *** segmentation violation > tr: Illegal byte sequence > > > > =========================================================== > There was a crash. > This is the entire stack trace of all threads: > =========================================================== > > Thread 1 (process 54446): > #0 0x00007fff830ec168 in wait4 () > #1 0x00007fff8e91a5f5 in system () > #2 0x0000000137a0b2f9 in TUnixSystem::StackTrace () > #3 0x0000000137a08e54 in TUnixSystem::DispatchSignals () > #4 <signal handler="" called=""> > #5 0x00000001379d9674 in TClass::GetStreamerInfo () > #6 0x0000000138925777 in TBufferFile::WriteClones () > #7 0x0000000138923d0a in TBufferFile::WriteObjectClass () > #8 0x0000000138923e26 in TBufferFile::WriteObjectAny () > #9 0x00000001379c1099 in TList::Streamer () > #10 0x0000000138923d0a in TBufferFile::WriteObjectClass () > #11 0x0000000138923e26 in TBufferFile::WriteObjectAny () > #12 0x0000000138923442 in TBufferFile::WriteFastArray () > #13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> () > #14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction () > #15 0x00000001389260ed in TBufferFile::ApplySequence () > #16 0x000000013892601d in TBufferFile::WriteClassBuffer () > #17 0x000000013948f180 in TTree::Streamer () > #18 0x0000000138960abc in TKey::TKey () > #19 0x00000001389367db in TFile::CreateKey () > #20 0x000000013892ea7e in TDirectoryFile::WriteTObject () > #21 0x000000013795928b in TObject::Write () > #22 0x00000001340266bf in XTreeSet::WriteTree () > #23 0x000000013405b2cf in XGenomeChip::ImportLayout () > #24 0x000000013403c9da in XDNAChip::Import () > #25 0x00000001340238fe in XManager::Import () > #26 0x000000013406956e in XSchemeManager::NewScheme () > #27 0x00000001340f3702 in ImportExonSchemes () > #28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, > op=0x1313ffb20, args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734 > #29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at > eval.c:635 > #30 0x00000001000a2176 in Rf_DispatchOrEval (call=0x7fff5fbfdc20, > op=0x7fff5fbfdc20, generic=0x7fff5fbfdc20 > "p?_=========================================================== > > > The lines below might hint at the cause of the crash. > If they do not help you then please submit a bug report at > http://root.cern.ch/bugs. Please post the ENTIRE stack trace > from above as an attachment in addition to anything else > that might help us fixing this issue. > =========================================================== > #5 0x00000001379d9674 in TClass::GetStreamerInfo () > #6 0x0000000138925777 in TBufferFile::WriteClones () > #7 0x0000000138923d0a in TBufferFile::WriteObjectClass () > #8 0x0000000138923e26 in TBufferFile::WriteObjectAny () > #9 0x00000001379c1099 in TList::Streamer () > #10 0x0000000138923d0a in TBufferFile::WriteObjectClass () > #11 0x0000000138923e26 in TBufferFile::WriteObjectAny () > #12 0x0000000138923442 in TBufferFile::WriteFastArray () > #13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> () > #14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction () > #15 0x00000001389260ed in TBufferFile::ApplySequence () > #16 0x000000013892601d in TBufferFile::WriteClassBuffer () > #17 0x000000013948f180 in TTree::Streamer () > #18 0x0000000138960abc in TKey::TKey () > #19 0x00000001389367db in TFile::CreateKey () > #20 0x000000013892ea7e in TDirectoryFile::WriteTObject () > #21 0x000000013795928b in TObject::Write () > #22 0x00000001340266bf in XTreeSet::WriteTree () > #23 0x000000013405b2cf in XGenomeChip::ImportLayout () > #24 0x000000013403c9da in XDNAChip::Import () > #25 0x00000001340238fe in XManager::Import () > #26 0x000000013406956e in XSchemeManager::NewScheme () > #27 0x00000001340f3702 in ImportExonSchemes () > #28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, > op=0x1313ffb20, args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734 > #29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at > eval.c:635 > =========================================================== > > Does anyone has any idea what that means? > > Do I need to re-install root again? > > Thanks > Assa > > > > On Mon, Sep 23, 2013 at 3:46 PM, cstrato <cstrato at="" aon.at=""> <mailto:cstrato at="" aon.at="">> wrote: > > Dear Assa, > > I assume that you get the error since you are mixing MoGene- 1_0-st > pgf-files with MoGene-2_0-st annotation files. > > For MoGene-2_0-st you need to do: > > scheme.mogene20st.na33 <- import.exon.scheme("__mogene20stv1", > filedir = file.path(scmdir, "na33"), > file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.clf"), > file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.pgf"), > > file.path(anndir, "MoGene- 2_0-st-v1.na33.2.mm10.__probeset.csv"), > file.path(anndir, "MoGene- 2_0-st-v1.na33.2.mm10.__transcript.csv")) > > For MoGene-1_0-st arrays you would need the MoGene-1_0-st annotation > files. > > Furthermore, your version of xps is pretty old, even for R-2.15.x. I > would suggest to update to the latest versions of R and xps. > > 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 <http: aon.at=""> > _._._._._._._._._._._._._._._.___._._ > > > > On 9/23/13 3:02 PM, Assa Yeroslaviz wrote: > > Hi everybody, > > I am trying to work with the xps package on mouse transcript > arrays but > having problem creating the root scheme. > > This is the command I am using to start with (taken from the scripts > given with the package) > > scheme.mogene10stv1.na33 <- import.exon.scheme("__mogene10stv1", > filedir = > file.path(scmdir, "na33"), > file.path(libdir, > "MoGene1_0_libFiles", > "MoGene-1_0-st-v1.r4.clf"), > file.path(libdir, > "MoGene1_0_libFiles", > "MoGene-1_0-st-v1.r4.pgf"), > file.path(anndir, > "MoGene-2_0-st-v1.na33.2.mm10.__probeset.csv"), > file.path(anndir, > "MoGene-2_0-st-v1.na33.2.mm10.__transcript.csv")) > > But when I am running this command I get the following error > massage: > Creating new file > </users>... > Importing > </users> > as <mogene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > New dataset <mogene-1_0-st-v1> is added to Content... > Importing > </users> > as <mogene-1_0-st-v1.anp>... > Note: The following header columns are missing or in wrong order: > <mouse_fl> > <mouse_mrna> > Number of probesets is <269751>. > <269751> records read...Finished > <269049> records imported...Finished > <215654> exon annotations imported. > Importing > </users> > as <mogene-1_0-st-v1.scm>... > Reading data from input file... > Number of probesets is <241576>. > Note: Number of annotated probesets <269751> is not equal > to number > of probesets <241576>. > <241576> records read...Finished > Sorting data for probeset_type and position... > Total number of controls is <45> > Filling trees with data for probeset type: control->chip... > Number of control->chip items is <0>. > Filling trees with data for probeset type: control->bgp... > Filling trees with data for probeset type: control->affx... > Number of control->affx probesets is <21>. > *Error: Number of control->affx imported <21> is not equal to > number of > annotated AFFX controls <167>.* > *Error: CDF with version/magic number > </users> > is not supported.* > *Error in import.exon.scheme("__mogene10stv1", filedir = > file.path(scmdir, : > error in function ?ImportExonSchemes?* > > > I would like to know what I am doing wrong and how to do it > right, so > that the scheme will be uploaded into R with the right > annotation files. > > Thanks > > Assa > > I'm working on MacBook Pro 10.7.5 > R session info - > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86___64 (64-bit) > > locale: > [1] > en_US.UTF-8/en_US.UTF-8/en_US.__UTF-8/C/en_US.UTF-8/en_US .UTF-__8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biobase_2.16.0 BiocGenerics_0.2.0 xps_1.16.0 > [4] BiocInstaller_1.4.9 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > >
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