I'm actually using MEDIPS to perform genome-wide methylation profile in satellite cells from normal animals. I have got a question regarding the way to normalize experimental rms regarding input rms. Is it possible to substract rms input score from the corresponding rms experimental condition? I was wondering whether it could be better to perform a differential coverage between experimental and input conditions and to keep only DMR regions. Thank you for your help Herv?? Acloque -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org.

Hi Herve, calculation of rms values for Input data and subsequent subtraction of IP and Input rms values is not recommended. I understand that you would like to identify enriched IP regions over Input? In section 7.7 of the MEDIPS manual, I briefly discuss experimental designs and Input data. Hopefully this will be helpful. Best regards, Lukas On Fri, Oct 25, 2013 at 2:31 AM, Herve Acloque [guest] < guest@bioconductor.org> wrote: > > I'm actually using MEDIPS to perform genome-wide methylation profile in > satellite cells from normal animals. I have got a question regarding the > way to normalize experimental rms regarding input rms. Is it possible to > substract rms input score from the corresponding rms experimental > condition? I was wondering whether it could be better to perform a > differential coverage between experimental and input conditions and to keep > only DMR regions. > > Thank you for your help > > Hervé Acloque > > -- 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]]