[BioC] Question about ChIPpeakAnno

[Martin Morgan]

On 06/06/2012 12:22 PM, Petros Kolovos wrote:
> Dear Julie
>
> the
> http://www.bioconductor.org/help/course-materials/2011/BioC2011/BioC2011_ChIPpeakAnno.pdf
> doesn't work. Could you please check it?

Hi Petros -- see

http://www.bioconductor.org/help/course-materials/2011/BioC2011/

and (I think)

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

Martin

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