advice for assessing concordance between primary capture and reciprocal capture results

Create issue
Issue #31 resolved
Former user created an issue


I was hoping for a few insights into how best to compare the results from our primary capture Hi-C experiment, and a reciprocal validation capture. The reciprocal experiment contained ~4000 baits.

As it is not advisable to compare the sets of stringent interactions directly, I have tried using the sdef package with published data. I've tried to reproduce the validation results presented in Javierre et al., but I do not arrive at perfectly agreeing values.

So my questions are: To prepare the matrix for input into sdef, should I include only the interactions which occur in both experiments and create an ID such as 'bait1_otherEnd1' etc? And then should I assess interaction p values, weighted P values, or CHiCAGO scores?

thanks! JB

Comments (2)

  1. Mikhail Spivakov

    We used all interactions that exceeded the score of zero (sic!) in at least one of the experiments (i.e., either primary or reciprocal) and exp(–Chicago_score) as input for baymod, setting p-value = TRUE. Note that we actually used a developmental version of this package, known as BGcom and available from here: I'm realising only now that it's not exactly identical to the one in sdef, although the differences are minor - so thanks for bringing this up.

  2. Log in to comment