Dear all,

please would you advise : could the normalization methods (TMM, etc) that are implemented in limma or edgeR (or DESeq2, or in other packages) be used for the normalization of 5C interaction data ? thanks, 

-- bogdan

Many of the considerations involved in normalization of Hi-C data are also likely to be applicable when normalizing 5C data. The question is whether you can assume that most loci pairs do not change in intensity between conditions. If so, you can use many of the methods described in the diffHic user's guide. If not... well, you're in trouble.