Hi,

I have a set of BS and oxBS treated samples from EPICarray and would like to analyze them using a R package. I found there are oxyBS and oxBS-MLE packages but I am struggling with their implementation to the analysis itself. For the methylation analysis I use the ChAMP and minfi packages so can anyone give me a hint how to combine those with any of the oxBS analyzing methods?

Or does anyone have a suggestion of any other analyzing method for assessing hydroxymethylation differences?

Thanks in advance!!

Sarka

Hello Sarka:

ChAMP indeed provided a way to  assessing hydroxymethylation differences, which is similar to DMP, just another way to implement this function to oxyBS data, Tiffany of ChAMP team also added a small paragraph in vignette to emphasis this. She is currently working on oxyBS data in Cambridge and is a real expert on that.

I am not that expert on oxyBS data, but I think most analysis could definitely be connected with ChAMP package, cause the data format and parameters are well designed, it's pretty easy to expend the functionality from ChAMP.

So I think you may:

1: Read the paragraph about oxyBS in ChAMP vignette, see if it help.

2: Connect Tiffany directly, she knows both ChAMP and oxyBS very well, she will provide you more idea analysis solution.

Best

Yuan Tian