[BioC] Question about ChIPpeakAnno

[Petros Kolovos]

Dear Julie,

Thank you very much

However I still cannot make the venn diagrams appeared with the
aforementioned code in the previous emails

 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!

I will post the session info ()

Thanks
Petros


> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
>