Resolution:
## Figure 3.
Multi-IP normalization. This figure shows CHANCE output for the multi-IP normalization module. (a-d) CHANCE produces a summary statement (a-b), a pairwise sample differential enrichment
matrix (c-d), and a graphical representation of the normalization process. The graphical
representation gives the same type of plot as in IP strength estimation for each IP
sample, as well as the consensus of the IP samples; see Materials and methods. The
summary statement quantifies the graphical representation by giving the statistical
significance of the difference of each sample from the consensus. The differential
enrichment matrix computes the percentage of the genome differentially enriched between
all pairs of samples, using the same technique for IP-Input comparison used in IP
strength estimation; see Materials and methods. (a,c,e) Multi-IP normalization of H3K4me1, H3K4me2, H3K4me3, and H3K36me3 in human embryonic
stem cells (H1 HESCs), from the Broad ENCODE data. (b,d,f) The capacity of CHANCE multi-IP normalization to detect batch effects. The clustering
of technical replicates (denoted by 1 and 2) for each biological replicate (denoted
by A and B) seen in (f) is quantified in the pairwise differential enrichment matrix
(d), which shows a statistically insignificant percentage of the genome differentially
enriched between replicates but a non-negligible percentage of the genome differentially
enriched between batches.
Diaz |