Narrow peaks, from the two replicates were compared using BEDtools (http://code.google.com/p/bedtools/), and only peaks that overlap between the two replicates were analyzed.
The three biological replicates were compared.
Upon meeting these criteria the independent biological replicates were compared, resolving 1016 SARs and 775 MARs along chromosome 16.
The averages of biological replicates were compared for the different strains and summarized as pie charts (Fig. 2 a).
In order to assess the difference between cell lines, the mutation rates of clone replicates were compared by the Welch two-sample t-test.
After normalization, the distributions of the expression values across replicates were compared before evaluating changes in transcription (Additional file 6).
In the Affymetrix analysis, G2 replicates were compared with G1 and G3, separately, and G3 replicates were compared with G1 to generate a list of differentially expressed genes.
The median values and 95% confidence intervals (CIs) (i.e., 2.5th and 97.5th percentiles) of these 2,000 bootstrap replicates were compared with the point estimates from the original data set.
In the examples described below, three replicates were compared.
Replicates were compared to the reference sequence to check for data reliability.
