Hello, 

I am looking for clarification and explanations for the following output headers of bumphunter DMR analysis:

Additionally, if a B=1000 permutation cut off was used, do the p values need to be further adjusted for multiple testing analysis or are they already corrected? 

thanks!

I would start by reading the Details section of the bumphunter help file. 

Regarding the table, each row is a candidate DMR.

value - is the average of the estimated coefficient (usually representing the difference between two groups) in the region

area - is the absolute value of the sum of the estimated coefficients in the region

cluster - the genome is divided into smaller regions, called clusters. We search for regions in each cluster to avoid going over a long stretch of the genome with no data. The value provided here is the ID for the cluster.

indexStart - is the index of the probe in the original methylation matrix where the region starts

indexEnd- is the index of the probe in the original methylation matrix where the region ends

L - is the number of probes in the region

clusterL - number of probes in the cluster

p.value - are explained in the help file. These do need multiple comparison corrections.

fwer - are explained in the help file. These do not need multiple comparison corrections