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.
>
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