Hi list What is the estimated fragment length in chip seq and how is this used in peak detection? What other files are used in calculating the false discover rate(FDR) in chip seq apart from the negative peak files? Thanks Harris -- output of sessionInfo(): None -- Sent via the guest posting facility at bioconductor.org.

Hi Harris, You need to contact the sequencing center that ran your samples to get the fragment length. Nobody here will be able to answer that question. As for the FDR, that depends on what you are talking about. You can compute the FDR for the peak detection, our you can compute the FDR from a comparison between sample types, in which case you will be using different samples. Best, Jim On Dec 27, 2013 3:41 PM, "George Harris [guest]" <guest@bioconductor.org> wrote: > > Hi list > What is the estimated fragment length in chip seq and how is this used in > peak detection? > What other files are used in calculating the false discover rate(FDR) in > chip seq apart from the negative peak files? > > Thanks > > Harris > > -- output of sessionInfo(): > > None > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]