[BioC] Question about ChIPpeakAnno

[Zhu, Lihua (Julie)]

Sorry, Petros!

It is - instead of _.

http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/ChI
PpeakAnno-BioC2011.pdf

For your other questions in a separate email, you need to give sessionInfo()
and tell us whether you are able to get the example work. Thanks!

Best regards,

Julie


On 6/6/12 3:22 PM, "Petros Kolovos" <p.kolovos at erasmusmc.nl> wrote:

> Dear Julie
> 
> the
> http://www.bioconductor.org/help/course-materials/2011/BioC2011/BioC2011_ChIPp
> eakAnno.pdf
> doesn't work. Could you please check it?
> 
> Best regards
> Petros
> 
> 
>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> 
> 
>