Question: Analyzing MeDIP-Chip data - using Affymetrix promoter array
8.9 years ago by
Adrian Johnson • 330
Adrian Johnson • 330 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.
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