How to calculate differential methylation with more than two groups?
Adeline M
Hello,
I am new to this field. I tried to find the answer to my question on the group, but I didn't really understand what I read.
I am trying to compare methylation between three groups. I have reached the stage where I need to use the calculateDiffMeth function. It works, but in the end, how can I know how the comparison was made, since there are more than two groups?
more than two groups detected:
will calculate methylation difference as the difference of max(x) - min(x),
where x is vector of mean methylation per group per region,but
the statistical test will remain the same.
Is there a way to specify in the final table what the meth.diff column corresponds to, i.e., group 1 vs. ctl, group 2 vs. ctl, or group 1 vs. group 2?
Thank you for your answer and have a nice day!
alex....@gmail.com
Hi Adeline,
There is currently no direct way or function to disentangle the results after running the multi-group comparison. Usually, we perform pairwise comparisons among the groups to obtain more detailed results.
See here for more detailed discusssion about that topic:
- https://groups.google.com/g/methylkit_discussion/c/mTpy8I9dJUk/m/ZkUPDF7qAQAJ
- https://groups.google.com/g/methylkit_discussion/c/-C1Ipkt3Vtc