Dear xps user/ developer,

My goal is to obtain a dataframe with all the statistics (fold changes
p-values etc) and annotation data (gene symbols etc). I need this dataframe
to select a subset hereof of 311 genes based on gene symbols.

The issue I have is as follows ( I use xps.pdf vignette var names to make
it easier to follow)

1) root scheme loaded for hgu133plus2
2) cel files imported (just 4 of them: 2 vehicle, 2 treated)
3) rma probe set normalized (data.rma)
4) filter operation: unifltr<-UniFilter  and: uniTest(unifltr) <-
c("t.test","two.sided","BH",0,0.0,FALSE,0.95,TRUE) for Mult Testing
correction (adjp)
5) this dataframe is fine:  tmp <- validData(rma.ufr)

adding phenotype data is the problem:
6)

tmp <- export.filter(rma.ufr, treetype="stt",
+
varlist="fUnitName:fName:fSymbol:fc:pval:flag",
+
as.dataframe=TRUE, verbose=FALSE)

the resulting data.frame in R memory and when I write it to disk is messed
up in certain rows ( clumps ALOT of rows in some rows in the 4th column)
and then clumps columns in 1 column at the end of the file.
Bit hard to explain exactly as I don't see the logic atm.


So then I tried removing the "FUnitName from the varlist because it seems
like unit_ID and unit_name are kinda redundant and I get a crash
(reproduced it 3 times with underlying code): I don't know if this is
relevant to the messed up data.frame, but added it just in case.

tmp<-export.filter(rma.ufr,treetype="stt",varlist="fName:fSymbol:fc:pval:flag",as.dataframe=TRUE,verbose=FALSE)

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f2bd8a26c3e in waitpid () from /lib/x86_64-linux-gnu/libc.so.6
#1  0x00007f2bd89acf5e in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#2  0x00007f2bd2ef6227 in TUnixSystem::StackTrace() () from
/home/winks/ROOT/root/lib/libCore.so
#3  0x00007f2bd2ef8aa3 in TUnixSystem::DispatchSignals(ESignals) () from
/home/winks/ROOT/root/lib/libCore.so
#4  <signal handler called>
#5  0x00007f2bd3852e92 in XUnivarSet::ExportUnivarTrees(int, TString*, char
const*, std::basic_ofstream<char, std::char_traits<char> >&, char const*)
() from /home/winks/R_HOME/library/xps/libs/xps.so
#6  0x00007f2bd377828d in XTreeSet::ExportTree(char const*, int, TString*,
char const*, std::basic_ofstream<char, std::char_traits<char> >&, char
const*) () from /home/winks/R_HOME/library/xps/libs/xps.so
#7  0x00007f2bd377cbe8 in XTreeSet::ExportTrees(char const*, char const*,
std::basic_ofstream<char, std::char_traits<char> >&, char const*) () from
/home/winks/R_HOME/library/xps/libs/xps.so
#8  0x00007f2bd377bcbc in XManager::Export(char const*, char const*, char
const*, char const*) () from /home/winks/R_HOME/library/xps/libs/xps.so
#9  0x00007f2bd3859034 in ExportData () from
/home/winks/R_HOME/library/xps/libs/xps.so
#10 0x00007f2bd8ffe7ba in ?? () from /usr/lib/R/lib/libR.so
#11 0x00007f2bd903668d in Rf_eval () from /usr/lib/R/lib/libR.so
#12 0x00007f2bd903bc03 in ?? () from /usr/lib/R/lib/libR.so
#13 0x00007f2bd911a0cc in ?? () from /usr/lib/R/lib/libR.so
#14 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#15 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#16 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#17 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#18 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#19 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#20 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#21 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#22 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#23 0x00007f2bd9039157 in ?? () from /usr/lib/R/lib/libR.so
#24 0x00007f2bd90394a5 in R_execMethod () from /usr/lib/R/lib/libR.so
#25 0x00007f2bd6399047 in ?? () from
/usr/lib/R/library/methods/libs/methods.so
#26 0x00007f2bd908b1e3 in ?? () from /usr/lib/R/lib/libR.so
#27 0x00007f2bd90365c9 in Rf_eval () from /usr/lib/R/lib/libR.so
#28 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#29 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#30 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#31 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#32 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#33 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#34 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#35 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#36 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#37 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#38 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#39 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#40 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#41 0x00007f2bd90730a3 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so
#42 0x00007f2bd9073330 in ?? () from /usr/lib/R/lib/libR.so
#43 0x00007f2bd90733c0 in run_Rmainloop () from /usr/lib/R/lib/libR.so
#44 0x000000000040078b in main ()
#45 0x00007f2bd898a76d in __libc_start_main () from
/lib/x86_64-linux-gnu/libc.so.6
#46 0x00000000004007bd in _start ()
===========================================================


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  0x00007f2bd3852e92 in XUnivarSet::ExportUnivarTrees(int, TString*, char
const*, std::basic_ofstream<char, std::char_traits<char> >&, char const*)
() from /home/winks/R_HOME/library/xps/libs/xps.so
#6  0x00007f2bd377828d in XTreeSet::ExportTree(char const*, int, TString*,
char const*, std::basic_ofstream<char, std::char_traits<char> >&, char
const*) () from /home/winks/R_HOME/library/xps/libs/xps.so
#7  0x00007f2bd377cbe8 in XTreeSet::ExportTrees(char const*, char const*,
std::basic_ofstream<char, std::char_traits<char> >&, char const*) () from
/home/winks/R_HOME/library/xps/libs/xps.so
#8  0x00007f2bd377bcbc in XManager::Export(char const*, char const*, char
const*, char const*) () from /home/winks/R_HOME/library/xps/libs/xps.so
#9  0x00007f2bd3859034 in ExportData () from
/home/winks/R_HOME/library/xps/libs/xps.so
#10 0x00007f2bd8ffe7ba in ?? () from /usr/lib/R/lib/libR.so
#11 0x00007f2bd903668d in Rf_eval () from /usr/lib/R/lib/libR.so
#12 0x00007f2bd903bc03 in ?? () from /usr/lib/R/lib/libR.so
#13 0x00007f2bd911a0cc in ?? () from /usr/lib/R/lib/libR.so
#14 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#15 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#16 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#17 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#18 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#19 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#20 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#21 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#22 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#23 0x00007f2bd9039157 in ?? () from /usr/lib/R/lib/libR.so
#24 0x00007f2bd90394a5 in R_execMethod () from /usr/lib/R/lib/libR.so
#25 0x00007f2bd6399047 in ?? () from
/usr/lib/R/library/methods/libs/methods.so
#26 0x00007f2bd908b1e3 in ?? () from /usr/lib/R/lib/libR.so
#27 0x00007f2bd90365c9 in Rf_eval () from /usr/lib/R/lib/libR.so
#28 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#29 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#30 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#31 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#32 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#33 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#34 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#35 0x00007f2bd90383a0 in ?? () from /usr/lib/R/lib/libR.so
#36 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#37 0x00007f2bd903988d in Rf_applyClosure () from /usr/lib/R/lib/libR.so
#38 0x00007f2bd9036350 in Rf_eval () from /usr/lib/R/lib/libR.so
#39 0x00007f2bd9038220 in ?? () from /usr/lib/R/lib/libR.so
#40 0x00007f2bd903646f in Rf_eval () from /usr/lib/R/lib/libR.so
#41 0x00007f2bd90730a3 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so
#42 0x00007f2bd9073330 in ?? () from /usr/lib/R/lib/libR.so
#43 0x00007f2bd90733c0 in run_Rmainloop () from /usr/lib/R/lib/libR.so
#44 0x000000000040078b in main ()
#45 0x00007f2bd898a76d in __libc_start_main () from
/lib/x86_64-linux-gnu/libc.so.6
#46 0x00000000004007bd in _start ()
===========================================================


winks@ubuntu:/media/Working Drive/Promotie/mArray biomarker study/Lisa
Paper/selection of genes$




thanks in advance
Steven Wink

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