[BioC] Ringo - finding enriched regions

[Hans-Ulrich Klein]

Hello,

I am confused about the results returned from the "findChersOnSmoothed" 
function in the Ringo package. I have an ExpressionSet object storing 
normalized log ratios (ChIP / Control) from three replicates. I use this 
analysis workflow:

 > eSetS = computeRunningMedians(eSet, probeAnno, modColumn="type",
                                winHalfSize=400, min.probes=5,
                                combineReplicates=TRUE)
[...]
 > y0 = upperBoundNull(exprs(eSetS), prob=0.99)
 > chers = findChersOnSmoothed(eSetS, probeAnno, thresholds=y0,
                              distCutOff=600, minProbesInRow=3)

Surprisingly, the first enriched region does not contain any probe 
intensity above the threshold y0. This applies to many regions called 
enriched.

 > chers[[1]]
BCR_ABL.chr1.cher1
Chr 1 : 10001787 - 10002329
Antibody : BCR_ABL
Maximum level = 1.665789
Score = 9.486747
Spans 15 probes.
 > y0
[1] 0.7279903
 > dim(eSetS)
Features  Samples
 4212009        1
 > exprs(eSetS[chers[[1]]@probes,])
         BCR_ABL
112645 0.2140274
112646 0.2469170
112647 0.2485301
112648 0.2501433
112649 0.2765225
112650 0.2813286
112651 0.2803291
112652 0.2727159
112653 0.2469170
112654 0.2469170
112655 0.1166212
112656 0.2355814
112657 0.2355814
112658 0.1608379
112659 0.2063285

Did I check the correct probes? Should not be the intensities > 0.727?

My Ringo version is 1.8.0.


Thanks in advance,
Hans-Ulrich



-- 
Hans-Ulrich Klein
Department of Medical Informatics and Biomathematics
University of Münster
Domagkstrasse 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405