[BioC] Ringo - finding enriched regions

[Joern Toedling]

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