Hi all,

Sorry in advance if this has been asked other places: we plotted heatmaps of H3K4me3 ChIP-seq signal with our interested regions in different mutants that we have, using the deepTools plotHeatmap function. Different mutants have different sets of regions being plotted. (some overlap between them but mostly distinct; the number of regions is also different)

Our interpretation of the data was that some mutant has more enrichment of the H3K4me3 signal than the other ones, based on the higher accumulation peak and a heatmap with a more distinct center line. I'm wondering if I'm misusing the tool/misinterpreting the data since we're supplying the program with different bed files --- the logic being that since they all seem to enrich the H3K4me3 signal, and each bed file contains a different amount of regions being plotted, thus naturally you will have a higher signal with samples with a bigger bed file.

I'm wondering what would be the best way to test this hypothesis that the interested regions of one mutant have higher H3K4me3 than the interested regions of other mutants. Would a t-test / anova do it? Any input would be greatly appreciated and please let me know if I can clarify anything.

Thanks! Jeff