Resolution:
## Figure 6.
Application to ChIP-Seq data. Shown are ECDF curves for P values resulting from comparisons of Pol-II ChIP-Seq data between replicates of the
same individual (first and second column) and between two different individuals (third
and forth column). The upper row corresponds to an analysis with DESeq ('D'), the lower row to one based on Poisson GLMs ('P'). If no true differential occupation
exists (that is, when comparing replicates), the ECDF (blue) should stay below the
diagonal (gray), which corresponds to uniform P values. In the first column, two replicates from HapMap individual GM12878 (A1) were compared against two further replicates from the same individual (A2). Similarly, in the second column, two replicates from individual GM12891 (B1) were compared against two further replicates from the same individual (B2). For DESeq, no excess of low P values was seen, as expected when comparing replicates. In contrast, the Poisson GLM
analysis produced strong enrichments of small P values; this is a reflection of overdispersion in the data, that is, the variance
in the data was larger than what the Poisson GLM assumes (see also Section Choice of distribution). The third column compares two replicates from individual GM12878 (A1) against two from the other individual (B1). True occupation differences are expected, and both methods result in enrichment
of small P values. The forth column shows the comparison of four replicates of GM12878
(A1 combined with A2) against four replicates of GM12891 (B1, B2); increased sample size leads to higher detection power and hence smaller P values.
Anders and Huber |