[BioC] Question about ChIPpeakAnno

[Petros Kolovos]

Dear Julie

the
http://www.bioconductor.org/help/course-materials/2011/BioC2011/BioC2011_ChIPpeakAnno.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
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
>