Hi! In running DiffBind on several peaksets, I've been using the "Fold" metric reported by the "dba.report" function, along with q-value thresholding, to determine differential enrichment. Based on Diffbind's online documentation, I understand this "fold" metric to be calculated by subtracting the normalized read count of Group 2 samples from that of Group 1 samples.
Since DeSeq2 (the analysis option I've been using in DiffBind) itself uses a log fold-change metric rather than a difference metric, I'm wondering why DiffBind uses a subtraction in its "Fold" calculation instead? Wouldn't you expect to get pretty different results? Or is it that the normalized read counts of Group 1 and Group 2 are log normalized already, and therefore that the fold difference and fold change values are mathematically equivalent through some sort of log arithmetic?