[BioC] xps library with mouse gene 1.0 transcript arrays
cstrato
cstrato at aon.at
Tue Sep 24 18:34:11 CEST 2013
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/ayeroslaviz/Documents/Annotations/xps/na33/mogene10stv1.root>...
> Importing
> </Users/ayeroslaviz/Documents/Annotations/xps/MoGene1_0_libFiles/MoGene-1_0-st-v1.r4.clf>
> 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 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/ayeroslaviz/Documents/__Annotations/xps//na33/__mogene10stv1.root>...
> Importing
> </Users/ayeroslaviz/Documents/__Annotations/xps//MoGene1_0___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/ayeroslaviz/Documents/__Annotations/xps/MoGene1.0___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/ayeroslaviz/Documents/__Annotations/xps//MoGene1_0___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/ayeroslaviz/Documents/__Annotations/xps//MoGene1_0___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
>
>
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