Yanara,

As Jianhong mentioned already, increasing totalTest will lead to a smaller p-value. Here is a previous post that might be helpful to you. Thanks!

https://stat.ethz.ch/pipermail/bioconductor/2010-November/036540.html

Best regards,

Julie


On 7/5/13 9:04 AM, "Ou, Jianhong" <Jianhong.Ou@umassmed.edu> wrote:

Hi Yanara,

Do you mean you have already figured out the error in makeVennDiagram? Could you share the reasons?

When you get p-value as 0, you could try a smaller totoTest number. The p-value is calculated by hypergeometric distribution function phyper (see ?phyper to get more details).
You can try to calculate p value by formula
p.value = phyper(overlaps - 1, peaksNumber2, totalTest - peaksNumber2, peaksNumber1,
            lower.tail = FALSE, log.p = FALSE)

Hope this could help you.

Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605

From: Yanara Marincevic-Zuniga <yanara_mz@hotmail.com>
Date: Thursday, July 4, 2013 11:05 AM
To: "Zhu, Lihua (Julie)" <Julie.Zhu@umassmed.edu>, Jianhong Ou <jianhong.ou@umassmed.edu>
Subject: RE: Venn diagrams using ChIPpeakAnno

Hi,

I managed to get a venndiagram (without any error codes) where I see that >34000 peaks overlap.
However, I get a p-value = 0.

I´ve tried changing totaltTest to a really high number as compared to the number of peaks in my two data sets, yet still the p-value remains as 0.


Do you have any suggestions to why this occurs?

Kind regrds,
Yanara M


________________________________
Subject: Fwd: Venn diagrams using ChIPpeakAnno
From: julie.zhu@umassmed.edu
Date: Thu, 4 Jul 2013 10:56:46 -0400
To: jianhong.ou@umassmed.edu; yanara_mz@hotmail.com

Jianhong,

Could you please help with this?

Thanks!

Julie

Begin forwarded message:

From: Yanara Marincevic-Zuniga <yanara_mz@hotmail.com>
Date: July 2, 2013, 8:25:55 AM EDT
To: "julie.zhu@umassmed.edu" <julie.zhu@umassmed.edu>
Subject: Venn diagrams using ChIPpeakAnno

Dear Julie,


I'm using ChIPpeakAnno (v 2.8.0) to annotate my peaks. To evaluate the overlap between replicates, I want to make a Venn diagram however I get following error code:



Error in seq.default(cnt, length.out = counts[i]) :
  length must be non-negative number
In addition: Warning message:
In phyper(p1.and.p2 - 1, p2, totalTest - p2, p1, lower.tail = FALSE,  :
  NaNs produced




Do you know why this occurs and what it means?

I'm thankful for any suggestions.


Kind regards,

Yanara M


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