Question: Analysis of DNA hydroxymethylation
gravatar for sarka.vorackova
2.2 years ago by
sarka.vorackova0 wrote:


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!!


champ minf oxybs oxbs-mle • 403 views
ADD COMMENTlink modified 2.2 years ago by Yuan Tian80 • written 2.2 years ago by sarka.vorackova0
Answer: Analysis of DNA hydroxymethylation
gravatar for Yuan Tian
2.2 years ago by
Yuan Tian80
Yuan Tian80 wrote:

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.


Yuan Tian

ADD COMMENTlink written 2.2 years ago by Yuan Tian80

Hi Yuan Tian,

thanks for such quick answer!!

I sure noticed that there is a paragraph in ChAMP vignette but I am not sure if it is suitable for my data.
I have 6 Sample Groups (samples with different mutations and normal) and for each sample I have BS and oxBS data. So first I need to asses BS-oxBS for each sample and than compare this hmC results between the Sample Groups.

Do you have any idea how to code this?

And how can I contact Tiffany? Do you maybe have her email adress?

Best regards,


ADD REPLYlink written 2.2 years ago by sarka.vorackova0
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