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In the correlation version (2), the genes defined connected if r>0.5.
(2) The correlation version brushes off negative correlations which may be very important, and the threshold 0.5 has no justification.
Thus, we instead use a Spearman rank correlation version of the rc, which doesn't assume any particular distribution, but rather the relative ranks of the expression values (for example if expression values for a set a genes were 5.74, 2.18, 3.65 and 9.13, then their ranks relative to one another would be 3, 1, 2 and 4).
In B. subtilis and V. cholerae this symmetry was made clearly visible, in the growth conditions used in this experiment, by the presence of a counter-diagonal in the map (running opposite to the continuous and strong signal that accounts for the contact between adjacent DNA segments; see also the correlation version of the contact map on Figure 1 figure supplement 3).
Similar(56)
Bivariate association between ordinal variables was assessed using Spearman's correlation (exact version).
Real time RT-PCR and microarray data were compared by Pearson correlation (SAS version 9.1 SAS Institute, Cary, NC) and eQTL were estimated as described above.
Correlations were analysed by Pearson correlations (SPSS version 19.0, SPSS Inc., Chicago, IL).
We used general estimating equations (GEE) to take into account possible intra-individual 'dependencies' or 'auto-correlation' (SAS Version 9.0, Cary, NC, USA) because many women contributed multiple data points to the analysis (mean 3.4, s.d. 1.4).
We find a significant correlation between this version of level of decentralization and the degree of property rights protection for privately run coal mines in each province.
Fundamentally r 2 is the squared correlation – the normalized version of the covariance, obtained by dividing covariance by the standard deviations of each of the variables.
We tested whether shape across the seven independent sub-elements covaried similarly by comparing the variance-covariance matrices using Mantel's test of matrix correlation in MANTEL version 1.15 [27] with 10,000 random row permutations of one of the matrices.
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