Dear Group, I am interested in identifying methylation changes in cell line after treating with estradiol. I have MCF10A cell line. I treated with two different concentrations of estradiol (concA, and concB). I want to identify methylation changes between no treatment and treatment and between two different concentrations. Controls: MCF10A + 5mC -> ChIP -> Chip MCF10A + IgG -> ChIP -> Chip Treatment MCF10A + 5 units of Estradiol -----> MeDIP -> Chip MCF10A + 8 units of Estradiol ------> MeDIP -> Chip First I want to be able to identify if 5mC is specific to methyl regions by comparing CEL file to IgG cel file. then I want to compare treatment vs control and later treatment vs treatment. I have been using MAT, but dont know how to make two controls in one tag file. Also I am not seeing much peaks. I would like to know if there are any methods in bioconductor that will help identify enriched peaks. Thank you. Ad.

Have you looked at the MEDME package? Michael On Fri, Mar 20, 2009 at 11:18 AM, Adrian Johnson <oriolebaltimore@gmail.com>wrote: > Dear Group, > I am interested in identifying methylation changes in cell line after > treating with estradiol. > > I have MCF10A cell line. I treated with two different concentrations > of estradiol (concA, and concB). I want to identify methylation > changes between no treatment and treatment and between two different > concentrations. > > > Controls: > MCF10A + 5mC -> ChIP -> Chip > MCF10A + IgG -> ChIP -> Chip > > Treatment > MCF10A + 5 units of Estradiol -----> MeDIP -> Chip > MCF10A + 8 units of Estradiol ------> MeDIP -> Chip > > > First I want to be able to identify if 5mC is specific to methyl > regions by comparing CEL file to IgG cel file. > then I want to compare treatment vs control and later treatment vs > treatment. > > I have been using MAT, but dont know how to make two controls in one > tag file. Also I am not seeing much peaks. > > I would like to know if there are any methods in bioconductor that > will help identify enriched peaks. > > Thank you. > > Ad. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]