[BioC] Ringo - finding enriched regions

[Hans-Ulrich Klein]

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
>>
>>     

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