[BioC] ChIPpeakAnno venn diagram statistics

[Ester Feldmesser]

Thank you very much for your answers and your patience.

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 12/7/2010 11:42 PM, Zhu, Lihua (Julie) wrote:
> 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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>>
>>      
>
>