[BioC] Question about ChIPpeakAnno

[Zhu, Lihua (Julie)]

Petros,

Totaltest specifies the total number of tests performed to obtain the list
of peaks. 

This is one of the frequently asked questions and many have contributed
wisdoms to address this question. Could you please take a look at the slides
at 
http://www.bioconductor.org/help/course-materials/2011/BioC2011/BioC2011_ChI
PpeakAnno.pdf, esp. the faq slide near the end?

Please do cc Bioconductor list (bioconductor
<bioconductor at stat.math.ethz.ch>) for sharing. Thanks!

Best regards,

Julie


On 6/6/12 11:02 AM, "Petros Kolovos" <p.kolovos at erasmusmc.nl> wrote:

> Dear Julie,
> 
> I would like to ask you also something else.
> 
> In the makeVennDiagrams function what do you mean by total tests?
> 
> For example i have the following code
> 
>> venn=makeVennDiagram(RangedDataList (pr, intron),NameOfPeaks =
>> c("peaks","intron"),maxgap = 0, totalTest = 320000)
> 
> PR=my peaks has 50000 peaks
> intron= table aquired from UCSC with all the exons 250000 peaks/coordinates
> 
> So how much should I put the totalTest
> 
> Is there a problem if I make a venn diagram of peaks vs introns?
> 
> Thanks
> 
> Best regards
> Petros
> 
> 
> 
>> Dear Petros,
>> 
>> You can safely ignore the warning message and proceed. I will modify the
>> code for the next release to replace multiple with select internally.
>> 
>> Best regards,
>> 
>> Julie
>> 
>> 
>> On 6/6/12 4:04 AM, "Petros Kolovos" <p.kolovos at erasmusmc.nl> wrote:
>> 
>>> Dear Dr Julie Zhu,
>>> 
>>> Good morning
>>> 
>>> My name is Petros Kolovos and I am a PhD student at Rotterdam,
>>> Netherlands.
>>> 
>>> I was using your library in order to annotate some chip peaks and in
>>> order
>>> to make some venn diagrams.
>>> 
>>> But I faced some problems with the venn diagrams
>>> 
>>> Here is what I am doing
>>> 
>>>> venn=makeVennDiagram(RangedDataList (pr, Anno_exon),NameOfPeaks =
>>> c("peaks","exon"),maxgap = 0, totalTest = 500000)
>>> Warning message:
>>> In findOverlappingPeaks(Peaks[[1]], Peaks[[2]], NameOfPeaks1 =
>>> NameOfPeaks[1],  :
>>>   Please use select instead of multiple!
>>> 
>>> What should I do?
>>> 
>>> Could you please help me as I am a rookie in this field
>>> 
>>> Thank you in advance
>>> 
>>> Yours sincerely
>>> Petros Kolovos
>>> 
>>> 
>>> 
>>> 
>> 
>> 
>> 
> 
>