[BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps

[Ou, Jianhong]

Hi Antonio, 

May I know the version of ChipPeakAnno you are using?

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Oct 1, 2012, at 10:36 AM, António Miguel de Jesus Domingues wrote:

> I've been trying to generate a set of high-confidence peaks that are common
> to my ChIP-seq replicates using ChipPeakAnno. The issue I'm having is
> matching the number of overlaping peaks seen on the venn digram resulting
> from:
> makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1","TF2"),
>        totalTest=(Npeaks1 + Npeaks2), useFeature=FALSE, minoverlap = 100,
> select= "first")
> 
> and the number of peaks ($MergedPeaks) from:
> findOverlappingPeaks(peaks1, peaks2, minoverlap = 100, select= "first",
> NameOfPeaks1="TF1", NameOfPeaks2="TF2")
> 
> I believe the difference is because some of peaks 2 overlap more than peaks
> in peaks1. Comparing peaks2 vs peaks one does not solve the problem and
> select= "first" is already being used. Also the $MergedPeaks data that is
> outputted from makeVennDiagram does not match the number of overlaps:
> $MergedPeaks
> RangedData with 18650 rows and 0 value columns across 24 spaces
> 
> [1] 19039
> [1] 21061
> $p.value
> [1] 0
> 
> $vennCounts
>     Replicate1 Replicate2 Counts
> [1,]          0          0  17300
> [2,]          0          1   3761
> [3,]          1          0   1739
> [4,]          1          1  17300
> attr(,"class")
> [1] "VennCounts"
> 
> 
> I would like to understand from where does this difference arises so that I
> ultimately have consistent results in visual and table format.
> 
> Cheers,
> António
> 
> 
> -- 
> -- 
> António Miguel de Jesus Domingues, PhD
> Neugebauer group
> Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
> Pfotenhauerstrasse 108
> 01307 Dresden
> Germany
> 
> e-mail: domingue at mpi-cbg.de
> tel. +49 351 210 2481
> The Unbearable Lightness of Molecular Biology
> 
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