[BioC] Ringo - finding enriched regions

[Joern Toedling]

Dear Hans-Ulrich,

in that case, I am afraid I cannot immediately tell you what the source of the
problem is. You are right, the smoothed probe intensities of these probes
should all be greater than y0. And in my analyses, I have never observed
something else. 
How do the ChIP-enriched region look like when you plot them?
(for example via
plot(chers[[1]], eSetS, probeAnno)
). If these plots indicate correct results than at least the positions of your
enriched regions seem to be correct and the problem is with assigning the
probe identifiers to the enriched regions.
There might be an issue with your probeAnno object and the way you generate it. 
What is the result of 
probeAnno["1.index"][probeAnno["1.start"]>=10001787 & 
probeAnno["1.start"]<=0002329]
? These probe identifiers should include the ones in the first enriched region.
I would suggest to use different probe names than "as.character" of the row
numbers. Due to R's implicit conversion between vector formats, such names
could lead to all sorts of hard-to-debug problems.
If you provide me with a short excerpt of your data and the example script, I
could have a deeper look into it to see where the problem might be.

Best regards,
Joern

On Tue, 20 Oct 2009 21:10:20 +0200, Hans-Ulrich Klein wrote
> Dear Joern,
> 
> the feature names of my ExpressionSet instance are:
> 
>  > all(featureNames(eSetS) == as.character(1:nrow(eSetS)))
> [1] TRUE
> 
> So in my case both expressions
>  > exprs(eSetS)[as.numeric(chers[[1]]@probes),]
> and
>  > exprs(eSetS)[chers[[1]]@probes,]
> return the same probes that have log ratios smaller than y0 as 
> described below.
> 
> Best wishes,
> Hans-Ulrich
> 
> Joern Toedling wrote:
> > Hello,
> >
> > I suspect that there is some issue with converting vectors between different
> > formats and the identifiers of your probes (the 'featureNames' of the
> > ExpressionSet) here.
> > The actual way to obtain those intensities with version 1.8.0 should be
> >
> > exprs(eSetS)[as.numeric(chers[[1]]@probes),]
> >
> > Please let me know if this does not give the expected results.
> >
> > However, I admit that providing indices as a character vector for the probes
> > slot was not necessary and rather misleading. Thus I have made slight changes
> > to the function and provided an additional method 'probes' which allows you to
> > obtain a character vector of probe names from each ChIP-enriched region
> > without having to access any slots directly.
> >
> > These changes can be found in the current development version 1.9.15, which
> > you can obtain from the Bioconductor repository tomorrow, and will also be in
> > the new release version (Ringo 1.10.0) at the end of this month.
> >
> > With the new version, the following is the preferred way for obtaining the
values:
> > exprs(eSetS)[probes(chers[[1]]),]
> >
> > Hope this helps.
> >
> > Best regards,
> > Joern
> >
> > On Mon, 19 Oct 2009 12:05:03 +0200, Hans-Ulrich Klein wrote
> >   
> >> 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


---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246926