Thanks, Julie.  If you notice, the second trial in my text file uses
totalTest=100000, which should be sufficient, right?

 

Ron

 

From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu] 
Sent: Monday, March 12, 2012 3:50 PM
To: Ron Hart
Cc: bioconductor@r-project.org
Subject: Re: question about makeVennDiagram

 

Dear Ron,

I noticed that you specified totalTest=100 which is too small for your
dataset. It should be larger than the largest peak number in your datasets. 

Here is a list of old posts on makeVennDiagram that should help you to
choose an appropriate number for totalTest.

-https://stat.ethz.ch/pipermail/bioconductor/2010-June/033941.html
-https://stat.ethz.ch/pipermail/bioconductor/2010-November/036540.html
-http://comments.gmane.org/gmane.science.biology.informatics.conductor/32345
-https://stat.ethz.ch/pipermail/bioconductor/attachments/20100905/bb689e19/a
ttachment.pl
-http://permalink.gmane.org/gmane.science.biology.informatics.conductor/2947
6
-
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/30115
-http://permalink.gmane.org/gmane.science.biology.informatics.conductor/3562
9
-http://comments.gmane.org/gmane.science.biology.informatics.conductor/34765

Best regards,

Julie


On 3/12/12 3:33 PM, "Ron Hart" <rhart@rci.rutgers.edu> wrote:

Hi Julie,
 
Once again, thank you for writing such a useful R package!  I'm working on
analyzing some data for another manuscript and I'm having trouble generating
a p-value from makeVennDiagram.  Enclosed is a text file with sample output.
 
Can you help me figure out why I get NaN for the p.value?  If it helps there
are something like 50,000 peaks per sample.
 
Thanks very much,
 
Ron
 
 


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