450K - ChAMP : How to analyse 5-hmc data ?

Question

[Nicolas Rosewick]

Hi,

I've a bunch of files (20 samples divided in two groups: untreated vs treated). For each sample I've the global methylation BS and the "true" methylation oxBS, all files in .idat. So to compute the methylation profile I used ChAMP on the oxBS data. It worked well. Now in order to check for hydroxyMethylation (5-hmc) I've to substract the oxBS data from the BS data. Is it possible with ChAMP ?

Thanks

Answer 1

[tiffany]

Hi,

ChAMP has a new function that helps you to do the subtraction. It's called champ.TrueMethyl() Be sure to have your samples labelled as BS or oxBS in the SampleGroup column of your sample sheet. Contact me at [e-mail] for anymore questions.

Best wishes, Tiffany