[BioC] ChIPpeakAnno venn diagram statistics

[Zhu, Lihua (Julie)]

I want to take this opportunity to thank Noah to share his insights and
experience using the ChIPpeakAnno package.

Ester, here is how the p-value is calculated for overlapping using your
given example, phyper(2577-1, 3912, totalTest-3912, 26009, lower.tail =
FALSE).

Best regards,

Julie


On 12/7/10 2:42 AM, "Ester Feldmesser" <ester.feldmesser at weizmann.ac.il>
wrote:

> Hello Noah,
> 
> I read the archives, but still there are some points that are not clear
> to me.
> 
> 1. How is the hypergeometric test implemented, in other words if we use
> the phyper R function,
> <http://127.0.0.1:26076/library/stats/html/Hypergeometric.html>what woud
> be p, m and k in the example given below.
> 
> 2. Has somebody any additional idea how to calculate the totalTest when
> comparing between the two different transcription factor peaks?
> 
> 3. Is there any other statistical test to calculate significance between
> overlaping peaks?
> 
> Thanks,
> 
> Esti
> 
> Ester Feldmesser, Ph.D.
> Bioinformatics Unit, Department of Biological Services
> Weizmann Institute of Science
> Levine Building, Room 110
> phone: +972-8-934-2614
> email: ester.feldmesser at weizmann.ac.il
> 
> He who thinketh he leadeth and hath no one following him is only taking a
> walk.
> Anonymous
> 
> 
> 
> On 12/6/2010 9:16 PM, Noah Dowell wrote:
>> Hello Ester,
>> 
>> Did you search the archives?  I commented on your question extensively and
>> Julie has also offered helpful insight and those messages are in the
>> archives.
>> 
>> Best,
>> 
>> Noah
>> 
>> 
>> On Dec 6, 2010, at 4:09 AM, Ester Feldmesser wrote:
>> 
>>    
>>> Hello,
>>> 
>>> I would like to understand how the hypergeometric test is applied in the
>>> makeVennDiagram function, specifically what is the total, the sample and the
>>> success groups.
>>> 
>>> Let's say we have two peak bed files with 3912 and 26009 peaks respectively
>>> and an overlap of 2577 peaks, how in this case should the test be applied?
>>> 
>>> Thank you,
>>> 
>>> Ester Feldmesser
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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>>>      
>>    
> 
> [[alternative HTML version deleted]]
> 
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