Hello there, At the moment, I use findOverlappingPeaks function to identified the overlapping peaks between two dataset A and B, and use makeVennDiagram to show the overlapping. However, I have find two problems 1) in findOverlappingPeaks function , multiple can be switched on to find multiple overlaps of B in A. However, there is no such option available in makeVennDiagram. This leads to inconsistent number of overlapping peaks output from findOverlappingPeaks and makeVennDaigram. How to solve this issue? 2) I also find that by swapping makeVennDiagram(RangedDataList(A, B), .....) and makeVennDiagram(RangedDataList(B, A), .....), the number of overlapping peaks is different. Why does it happen? and what is the proper way to do use makeVennDiagram() function? Thanks for any suggestions. Regards, Binbin

Binbin, Thank you very much for the feedback and great suggestions! 1) We could add multiple as a parameter in the makeVennDiagram function. However, the significance test should not be based on multiple=yes since you might count some peaks multiple times simply because one peak in one dataset overlaps multiple peaks in another dataset. 2) When there are multiple peaks from one dataset (A) overlap with one peak from the other dataset (B), the number of overlap will depend on the order of the list RangedDataList(A, B) vs RangedDataList(B, A). I would suggest use the smaller number resulted from the order RangedDataList(B, A). We could implement this inside the function to make it more user friendly if that is useful. Best regards, Julie On 12/6/10 10:15 AM, "Binbin Liu" <b.b.liu at="" leeds.ac.uk=""> wrote: > Hello there, > > At the moment, I use findOverlappingPeaks function to identified the > overlapping peaks between two dataset A and B, and use makeVennDiagram to show > the overlapping. However, I have find two problems > > 1) in findOverlappingPeaks function , multiple can be switched on to find > multiple overlaps of B in A. However, there is no such option available in > makeVennDiagram. This leads to inconsistent number of overlapping peaks output > from findOverlappingPeaks and makeVennDaigram. How to solve this issue? > > 2) I also find that by swapping makeVennDiagram(RangedDataList(A, B), .....) > and makeVennDiagram(RangedDataList(B, A), .....), the number of overlapping > peaks is different. Why does it happen? and what is the proper way to do use > makeVennDiagram() function? > > > Thanks for any suggestions. > > Regards, > Binbin > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Binbin, In the middle of code change, I realized that it does not make sense to add multiple=T since all the venn count will be wrong. Let us take an extreme example, peak list A contains 1 peak and peak list B contains 100 peaks. Let us say 2 of the 100 peaks in B overlap the peak in A. If allowing multiple overlap, then the number of overlap in the venn diagram would be 2 which is bigger than the number of peaks in A. This not only makes the venn diagram look odd, but also throws the stats off. So I decide not to implement multiple = T in makeVennDiagram. Make sense? Thanks again for the feedback! Best regards, Julie On 12/6/10 12:10 PM, "Binbin Liu" <b.b.liu at="" leeds.ac.uk=""> wrote: > Hi Julie, > > Yes, it would be great if multiple=T can be implemented into > makeVennDiagram(). Please let me know when I need to upgrade my existing > version of ChIPpeakAnno > > > Many thanks.. > > Binbin > > On 6 Dec 2010, at 16:39, Zhu, Lihua (Julie) wrote: > >> Binbin, >> >> Thank you very much for the feedback and great suggestions! >> >> 1) We could add multiple as a parameter in the makeVennDiagram function. >> However, the significance test should not be based on multiple=yes since you >> might count some peaks multiple times simply because one peak in one dataset >> overlaps multiple peaks in another dataset. >> >> 2) When there are multiple peaks from one dataset (A) overlap with one peak >> from the other dataset (B), the number of overlap will depend on the order >> of the list RangedDataList(A, B) vs RangedDataList(B, A). I would suggest >> use the smaller number resulted from the order RangedDataList(B, A). We >> could implement this inside the function to make it more user friendly if >> that is useful. >> >> Best regards, >> >> Julie >> >> >> On 12/6/10 10:15 AM, "Binbin Liu" <b.b.liu at="" leeds.ac.uk=""> wrote: >> >>> Hello there, >>> >>> At the moment, I use findOverlappingPeaks function to identified the >>> overlapping peaks between two dataset A and B, and use makeVennDiagram to >>> show >>> the overlapping. However, I have find two problems >>> >>> 1) in findOverlappingPeaks function , multiple can be switched on to find >>> multiple overlaps of B in A. However, there is no such option available in >>> makeVennDiagram. This leads to inconsistent number of overlapping peaks >>> output >>> from findOverlappingPeaks and makeVennDaigram. How to solve this issue? >>> >>> 2) I also find that by swapping makeVennDiagram(RangedDataList(A, B), .....) >>> and makeVennDiagram(RangedDataList(B, A), .....), the number of overlapping >>> peaks is different. Why does it happen? and what is the proper way to do use >>> makeVennDiagram() function? >>> >>> >>> Thanks for any suggestions. >>> >>> Regards, >>> Binbin >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > >