xps library with mouse gene 1.0 transcript arrays
1
0
Entering edit mode
Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 5 weeks 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 • 1.6k views
ADD COMMENT •
0
Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 7.1 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
ADD COMMENT •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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 > >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1710 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6