[BioC] xps: root.profile on a asubset of the data

Mon Aug 23 11:32:09 CEST 2010

Dear Christian,

Many thanks for making some code changes, thats great.  Unfortunately I
have tried it and it doesn't seem to work.

I create a list of the tree nodes:
> samples <- unlist(treeNames(rootData))

Then check to see if I can use the root graphics:
> root.image(rootData,treename = samples[1])
> root.profile(rootData,treename=samples[1])

But when I try to do a root.profile with more in it I get an error:
> root.profile(rootData,treename=samples[1:2])
root [0]
Processing
/Users/dbrewer/Library/R/2.11/library/xps/rootsrc/macroDrawProfilePlot.C("/Users/dbrewer/Library/R/2.11/library/xps/libs/i386/xps.so","/Volumes/Datastore/ProstateCancerMap/QCFINAL/cancermapQC_cel.root","ProfilePlot","DataSet","0309_CoC(3)41_ExH_PRC133:0309_CoC(3)42_ExH_PRC134","cel","fInten","",0,0,1,1,1,800,600)...
Warning in <TParallelCoord::TParallelCoord>: Call
tree->SetEstimate(tree->GetEntries()) to display all the tree variables
Error in <TTreeFormula::AnalyzeFunction>: We thought we had a function
but we dont (in 0309_CoC(3)41_ExH_PRC133.fInten)

Error in <TTreeFormula::Compile>:  Bad numerical expression :
"0309_CoC(3)41_ExH_PRC133.fInten"
Warning in <TParallelCoord::AddVariable>:
log(0309_CoC(3)41_ExH_PRC133.fInten) could not be evaluated
Error in <TTreeFormula::AnalyzeFunction>: We thought we had a function
but we dont (in 0309_CoC(3)42_ExH_PRC134.cel.fInten)

Error in <TTreeFormula::Compile>:  Bad numerical expression :
"0309_CoC(3)42_ExH_PRC134.cel.fInten"
Warning in <TParallelCoord::AddVariable>:
log(0309_CoC(3)42_ExH_PRC134.cel.fInten) could not be evaluated

 *** Break *** bus error
/Volumes/Datastore/ProstateCancerMap/QCFINAL/2278: No such file or
directory.
Attaching to process 2278.
Reading symbols for shared libraries . done
Reading symbols for shared libraries
.......................................... done
0x94bc7189 in wait4 ()

========== STACKS OF ALL THREADS ==========

Thread 1 (process 2278 thread 0x10b):
#0  0x94bc7189 in wait4 ()
#1  0x94bc4cd4 in system$UNIX2003 ()
#2  0x00906141 in TUnixSystem::StackTrace ()
#3  0x00909ac5 in TUnixSystem::DispatchSignals ()
#4  0x00909c38 in SigHandler ()
#5  <signal handler called>
#6  0x048bd989 in TParallelCoordEditor::SetModel ()
#7  0x044ecf41 in TGedEditor::ConfigureGedFrames ()
#8  0x044eda3a in TGedEditor::SetModel ()
#9  0x04556eee in G__G__Ged_221_0_28 ()
#10 0x01077e27 in Cint::G__CallFunc::Execute ()
#11 0x008eec7f in TCint::CallFunc_Exec ()
#12 0x0086b002 in TQConnection::ExecuteMethod ()
#13 0x0086fd45 in TQObject::Emit ()
#14 0x00429bce in TCanvas::Selected ()
#15 0x048b1c62 in TParallelCoord::Draw ()
#16 0x03b44fd9 in XPlot::DrawParallelCoord ()
#17 0x03c9128f in G__xpsDict_564_0_22 ()
#18 0x010750c2 in Cint::G__ExceptionWrapper ()
#19 0x01148021 in G__execute_call ()
#20 0x011484ed in G__call_cppfunc ()
#21 0x0111bd4e in G__interpret_func ()
#22 0x01106d7b in G__getfunction ()
#23 0x0121b96b in G__getstructmem ()
#24 0x0121161b in G__getvariable ()
#25 0x010d3931 in G__getitem ()
#26 0x010d6839 in G__getexpr ()
#27 0x0117fc11 in G__exec_statement ()
#28 0x0111df95 in G__interpret_func ()
#29 0x011072f5 in G__getfunction ()
#30 0x010d3a74 in G__getitem ()
#31 0x010d6839 in G__getexpr ()
#32 0x010e9c79 in G__calc_internal ()
#33 0x0118e40c in G__process_cmd ()
#34 0x008f21c4 in TCint::ProcessLine ()
#35 0x008f0f1f in TCint::ProcessLineSynch ()
#36 0x008388b0 in TApplication::ExecuteFile ()
#37 0x0083759d in TApplication::ProcessLine ()
#38 0x00031799 in TRint::Run ()
#39 0x00001bae in main ()
Root > Function macroDrawProfilePlot() busy flag cleared

installed.packages() indicates xps is version 1.8.3

Thanks

Dan

On 22/08/2010 6:49 PM, cstrato wrote:
> Dear Daniel,
> 
> Sorry my mistake again!
> After looking at my source code I realized that currently it is not
> possible to use a subset of trees only. Thus I have just uploaded to
> Bioconductor a new version "xps_1.8.3" which should solve the problem,
> and will be available within the next 1-2 days. You should now be able
> to use parameter "treename" to plot only a subset of trees.
> 
> Please let me know if the new version solves your problem.
> Especially I am interested to know how many treenames you can pass to
> function root.profile() since there could be a limit on the number of
> characters you can pass to the root macro.
> 
> Since you mention that there are too many arrays to look reasonable on
> one plot, you could also change parameter "w" from the default "w=800"
> to e.g. "w=4000", especially if you save the plot by setting e.g.
> "save.as='png'".
> 
> Best regards
> Christian
> 
> 
> On 8/20/10 5:35 PM, Daniel Brewer wrote:
>> Hi Christian,
>>
>> I tried that, but it kicked up an error and only plotted one boxplot.
>> It was like "treename" could only take one parameter.  Maybe I was doing
>> something wrong.  I will have another go.
>>
>> Dan
>>
>> On 20/08/2010 4:06 PM, cstrato wrote:
>>> Dear Daniel,
>>>
>>> You can simply use parameter "treename" to plot only a subset of trees,
>>> see "?root.profile".
>>>
>>> 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 8/20/10 4:47 PM, Daniel Brewer wrote:
>>>> Hello,
>>>>
>>>> I am using xps to do some quality control on an Affymetrix exon array
>>>> experiment I am looking at.  I am trying to use the ROOT graphics to
>>>> plot density boxplots of the raw intensities (using root.profile).  The
>>>> problem is that there is too many arrays to look reasonable on one
>>>> plot.
>>>>    Is there a way to split up the dataset into smaller pieces and plot
>>>> them?
>>>>
>>>> Thanks
>>>>
>>>> Dan
>>>>
>>

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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