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Question: Analyzing MeDIP-Chip data - using Affymetrix promoter array
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gravatar for Adrian Johnson
8.7 years ago by
Adrian Johnson330 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.
ADD COMMENTlink modified 8.7 years ago by Michael Lawrence620 • written 8.7 years ago by Adrian Johnson330
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gravatar for Michael Lawrence
8.7 years ago by
Michael Lawrence620 wrote:
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]]
ADD COMMENTlink written 8.7 years ago by Michael Lawrence620
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