Problem with methykit installation

[Dilraj kaur]

Hi,

I am trying to analyse my sample files from Bismark methylation coverage output in methyl kit.

I am facing 2 issues.

The first one is methylkit, which is not installable. like i have tried on multiple R versions and multiple R platforms. It always throws errors.

The other one is that my samples are not united, which means I have around 17 samples from different sources and want to cluster them and make PCA and cluster, but again, it's not working. Just a conceptual question, if the treatment group and control group of different organisms, will this work?

Regards

Dr. Dilraj kaur

[Alexander Blume]

Hi Dilraj,

Thanks for using methylKit. Could you please share a few more details to help troubleshoot? If possible please also share the code that led to the errors. 

What exact errors do you get when installing methylKit, and which R versions have you tried? 

When uniting samples, what’s the error or issue you're seeing? What are the different sources you are referring to? Are you only analyzing CpG methylation or are you trying to mix different cytosine contexts?

Regarding your conceptual question, what organisms are you comparing, and are treatment/control from different species or just different conditions?

Best,

Alex

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