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

Mon Aug 23 20:00:58 CEST 2010

Dear Daniel,

The reason for the error messages you get is that the names of your 
CEL-files contain parenthesis which cause the ROOT C++ class 
TParallelCoord to interpret the names as formulas, since TParallelCoord 
allows you to pass an expression.

In my C++ code I am even taking advantage of this possibility and pass 
"varexpr=log(celname)" if parameter "as.log=TRUE".

I am afraid that the only possibility to solve this problem is to change 
the names of the CEL-files when importing them as trees into the ROOT 
file, however you do NOT need to change the names of the original 
CEL-files.

Since I know that many CEL-files contain strange names with many 
problematic characters (e.g. 
"42A#0214(12);06/23/99;MES-SA/Dx-batch#21089.CEL") I have implemented 
the possibility to use more informative names as aliases when importing 
the CEL-files.

For example to confirm the error messages you get I have renamed two of 
the four test CEL-files (TestA1.CEL, TestA2.CEL, TestB1.CEL, TestB2.CEL) 
as follows:

# first, import ROOT scheme file
 > scheme.test3 <- 
root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))

# import CEL files with new names
 > celdir <- "/Volumes/CoreData/ROOT/rootdata/testAB/raw"
 > celnames <- c("TestA1", "TestA2", "0309_CoC(3)41_ExH_PRC133", 
"0309_CoC(3)42_ExH_PRC134")
 > data.test3 <- import.data(scheme.test3, "tmp_Test3", celdir=celdir, 
celnames=celnames)

# this profile plot is ok
 > root.profile(data.test3, treename=c("TestA1.cel", "TestA2.cel"))

# this profile plot reproduces the error messages you get
 > root.profile(data.test3, treename=c("0309_CoC(3)41_ExH_PRC133.cel", 
"0309_CoC(3)42_ExH_PRC134.cel"))

# you can always extract the names of the original CEL-files
 > rawCELName(data.test3, fullpath=FALSE)
[1] "TestA1.CEL" "TestA2.CEL" "TestB1.CEL" "TestB2.CEL"

I hope this helps you to understand the reason of the problem, and that 
my only advice can be to change the name of the CEL-files during import 
(it is not possible to change the tree names once they are imported into 
a ROOT file).

Best regards
Christian

On 8/23/10 11:32 AM, Daniel Brewer wrote:
> 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
>>>>>
>>>
>