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Bioo Scientific Launches DNA Methyl-Seq Kit for NGS Methylome Analysis Bioo Scientific Vendor Forum 0 03-30-2012 01:04 PM
PubMed: Methyl-Analyzer--whole genome DNA methylation profiling. Newsbot! Literature Watch 0 02-11-2012 12:51 AM

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Old 03-02-2017, 05:23 AM   #1
dclayton
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Default Comparing multiple treatment groups for DNA methylation (RRBS, methyl kit, GLM)

We have an RRBS dataset with 4 treatment groups, n=6 samples each group. I'd like to be able to do an ANOVA-style first stage analysis to look for evidence that treatment effects exist in the dataset as a whole, before moving forward into pairwise post-hoc analyses. We've been using Methylkit (beta binomial distribution) for pairwise analyses, but unless I'm mistaken it doesn't support multi-group comparisons. Is there another package that does? Or is this something we would have to develop on our own (as a GLM in R for example)? Advice appreciated!
-david
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