My apologies Jianhong,

I forgot to attach the session info. I am using ChIPpeakAnno_2.5.12

Just an extra information, using the example from the vignette, it does
work as it should but that might be simply because the overlaps are more
straightforward - that is, no peak in peaks1 overlap with more than one
peak in peaks2 and vice-versa.

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid      grDevices datasets  graphics  utils     stats     methods
[8] base

other attached packages:
 [1] ChIPpeakAnno_2.5.12                 limma_3.12.3
 [3] org.Hs.eg.db_2.7.1                  GO.db_2.7.1
 [5] RSQLite_0.11.2                      DBI_0.2-5
 [7] AnnotationDbi_1.18.4                BSgenome.Ecoli.NCBI.20080805_1.3.17
 [9] BSgenome_1.24.0                     GenomicRanges_1.8.13
[11] Biostrings_2.24.1                   IRanges_1.14.4
[13] multtest_2.12.0                     biomaRt_2.12.0
[15] VennDiagram_1.5.1                   ggplot2_0.9.2.1
[17] Biobase_2.16.0                      BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] amap_0.8-7         colorspace_1.1-1   dichromat_1.2-4
DiffBind_1.2.4
 [5] digest_0.5.2       edgeR_2.6.12       gdata_2.12.0
gplots_2.11.0
 [9] gtable_0.1.1       gtools_2.7.0       labeling_0.1
MASS_7.3-21
[13] memoise_0.1        munsell_0.4        plyr_1.7.1
proto_0.3-9.2
[17] RColorBrewer_1.0-5 RCurl_1.91-1       reshape2_1.2.1
scales_0.2.2
[21] splines_2.15.1     stats4_2.15.1      stringr_0.6.1
survival_2.36-14
[25] tools_2.15.1       XML_3.9-4          zlibbioc_1.2.0



On 1 October 2012 16:54, Ou, Jianhong <Jianhong.Ou@umassmed.edu> wrote:

> Hi Antonio,
>
> May I know the version of ChipPeakAnno you are using?
>
> Yours sincerely,
>
> Jianhong Ou
>
> jianhong.ou@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@mpi-cbg.de
> > tel. +49 351 210 2481
> > The Unbearable Lightness of Molecular Biology
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
-- 
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@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

	[[alternative HTML version deleted]]

