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

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