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@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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>>      
>    

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