[BioC] Ringo - finding enriched regions
Hans-Ulrich Klein
h.klein at uni-muenster.de
Mon Oct 19 12:05:03 CEST 2009
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
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