10 days ago by
CRUK, Cambridge, UK
Looking at your PCA, I see no evidence that the components are in the wrong order. The first component is capturing most of the biological variance you expect, however there is one sample (red in the plot you sent me) where the two replicates have greater variance between them than the sample groups have between each other. The high variance between these two samples is indicative of something unexpected going on in the experiment. This is likely something technical in the ChIP (or peak calling is this is a peak score plot) and worth trying to get to the bottom of. You may want to look at these two ChIPs in a browser, and compare the peaks called for each of them (eg using Venn diagrams). If this is a peak score plot, it would be interesting to compare to a read score plot -- if they show less variance using read scores, that indicates the issue is in peak calling, which is less of a concern.