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 [[alternative HTML version deleted]]