Chr.xxxx Position ColumnID  For cluster building, bumphunter needs the genomic
position of the individual oligos. Define the feature annotation colum which contains this paramter. bumphunter expects the cooridinates given in a fomat: "chromosome.baseposition" (e.g. "chr1.00123456" or "01.00123456" or "001.0012345600123490" in all cases bumphunter would extract "00123456" as feature position, chromosome id can be neglectid for cluster building). You might use use main menu  Adjust  Annotation  function to create such a parameter. bumphunter expects data to be sorted in increasing order. If not yet done, sort the matrix now (Main menu adjust annotation  Sort) You might also sort the cooridinates on the fly for this particular analysis: Define "001.00123456:sort". 
MaxGap  The maximum distance between two neighbouring oligos which are contained in the same cluster Small MaxGap will generate less but dense, smaller clusters Larger MaxGap will generate more, larger and wide spread clusters To see the effect of MaxGap specify Action : "clusterscan" 
pAveraging method  Define how to compute average pvalue for a cluster.

Regulation Averagin method  Define how to compute average regulation for a cluster. In case of log2values (or other signed data) you should NOT use geometric mean (e.g. Mvalues). 
Permutation file name  A permutation data file created previously with SUMO !!! NB: the permutation values MUST have the same (sorted) order of features as the data used for bumphunter NB !!! 
Action  What to do:

ClusterID  (Random) unique ID for each cluster  
OriginalRow  Row number of the respective feature in the original data matrix  
pCluster  mean pvalue for the cluster as computed from te cluster members. Obviously pmean will be identical for all members of the same cluster  
Signal  Mean "signal" (e.g. ClassMean difference) for the cluster as computed from te cluster members. Obviously  see above.  
pPerm  p value from permutation test. Always "0" if no permutation test was performed. 