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The maximum FPC-based correlation was almost equal to the ordinary correlation (r=0.853 restricted to TSS regions, r=0.796 overall).
Phi correlation is a special case from the Pearson Product Moment correlation applied to data containing dichotomies [ 3] and is generated by the ordinary correlation formula generally used in factor analysis programs.
We then calculated pairwise correlations between principal component scores for all the components, detecting significant correlations (Bonferroni corrected P≤10−6) at higher-order components in the TSSs, that could not have been observed applying the ordinary correlation merely based on the read-enrichment in whole regions.
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Similarly, we detected significant correlations between H3K36me3 and other chomatin marks such as H3K4me3 and H3K9ac in the first component, which cannot be revealed using correlation coefficients based on the ordinary coverage correlation.
Since Spearman rank correlation describes the monotonicity of bivariate relationship and is not sensitive to high leverage points this measure was preferred to the ordinary linear correlation coefficient.
We have shown how this methodology can outperform ordinary correlation measurements to uncover correlations between histone marks that are similarly regulated but which do not directly co-localize.
Among the many analytical techniques available, the Local Similarity Analysis LSAA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis.
Using the microbial community and gene expression datasets, we demonstrated that eLSA uniquely captures additional time-dependent associations, including local and time-delayed association patterns, when compared to ordinary correlation methods, such as PCC.
The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis.
To address potential shortcomings with respect to a biologically inadequate reflection of CN and GE abnormalities by ordinary correlation analysis, Schäfer et al. [ 29] substitute sample means by the reference medians, and Lipson et al. [ 30] use quantile-based analysis to obtain improved correlation coefficients.
Correction for overlap is necessary because ordinary correlations between an item and the scale of which it is a part are spuriously inflated.
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