[BioC] ChIPpeakAnno-makeVennDiagram question

[Zhu, Lihua (Julie)]

Camila,

TotalTest needs to be at least as large as the number of peaks in
CNSallPeaks_rd and OPColig2Peaks_rd. For example, if there are 1000 peaks in
CNSallPeaks_rd and 2000 peaks in OPColig2Peaks_rd, then totalTest needs to
be >= 2000.

For details, please refer to an old post at
http://grokbase.com/t/r/bioconductor/123cz0jc0b/bioc-question-about-makevenn
diagram. Thanks!

Best regards,

Julie


On 8/15/13 6:08 PM, "Camila Lopez-anido" <lopezanido at wisc.edu> wrote:

> Hi, 
> 
> I'm a graduate student at the UW-Madison, and I'm getting an error message
> when I use makeVennDiagram() -I was wondering if there is a simple solution? I
> saw that someone else had asked about something related (similar message)
> online, but I couldn't find how they fixed the problem?
> 
> 
> I inputed two RangedData files, which I successfully performed
> findOverlappingPeaks() with:
> 
> 
>> makeVennDiagram(RangedDataList(CNSallPeaks_rd, OPColig2Peaks_rd),
>> NameOfPeaks=c("CNSall","OPColig2"), maxgap=0, minoverlap=1, totalTest=100,
>> cex=1, counts.col="red", useFeature=FALSE)
> 
> 
> #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
> 
> 
> 
> Is there a simple solution to this?
> 
> 
> Thanks, 
> Camila Lopez-Anido