Entering edit mode
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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