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In these experiments, the Pearson correlation coefficient between two technical replicates varied between 0.994 and 0.999 (Fig. S1A), ensuring the confidence of the dataset for further analysis.
b) Correlation coefficient between two technical replicates of gels from a given cell line.
The correlation coefficients between two technical replicates of gels from each cell line were also determined.
The data was first reduced to mono-tissue by taking average of each probe set between two technical replicates.
We found no major difference in coverage efficiency between two technical replicates, indicating that all four technologies give high technical reproducibility.We next evaluated coverage efficiency as a function of sequencing depth.
The Poisson distribution appears to describe well the variation observed between two technical replicates of the same specimen, i.e., two aliquots of the same library allocated to two lanes on a flow cell [ 3- 5].
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The error bars in figure 3 represent the standard deviation between three technical replicates in one representative experiment.
Probes that are up or down regulated more that 1.5 fold and who's SEM indicate agreement between three technical replicates are shown.
We investigated the reproducibility of the QPCRs, using the same 96 primer pairs that were used for the uniformity experiments, by comparing Ct values between five technical replicate plates and found coefficients of variation to be low.
The non-reference allele frequencies were very consistent between the two technical replicates, as illustrated in Figure 3 with high Pearson correlation coefficient (R = 0.96).
The quantitative PCR assay provides reasonable resolution, however, as determined by variation between the two technical replicates performed for each individual in the current study.
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