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kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
MIT License
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Can dmrseq be used on several groups but single sample in each group ? #63

Closed DengEr-1993 closed 6 months ago

DengEr-1993 commented 6 months ago

Hello there,

I have a question about dmrseq() function in this package.

There are 5 groups and more than 2 replicates in each group. I have idea that if dmrseq() can compare single sample between groups?

Because I want to use the average value of replicates in each group to visualize similar result between groups.

I tried to do this but it doesn't work through dmrseq(). Maybe it needs replicates to do differential analysis.

Another questions is if I can compare these expression level of single sample between groups, I should calculate the average values of Coverage and methylation, respectively. It is a little complicated.

But it doesn't matter. Could you just give me some advice on my first question ?

Thank you very much.

Best, xiangyi

kdkorthauer commented 6 months ago

Hi Xiangyi,

dmrseq requires replicates in each group to perform statistical inference. Comparisons of single samples is not possible with this methodology.

Best, Keegan