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3.3.11.1 Calculating correlations

Assuming that such paired profiles have been loaded within VAMP (see section 4.4 for an example), the analysis can be launched from the menu Tools $\rightarrow $ Correlation Analysis $\rightarrow $ Compute:

Figure 3.67: - ``Compute'' Dialog for Correlation Analysis.
Image gtca-compute-dialog

Several parameters can be chosen to run a Correlation Analysis

scope:
should correlation coefficients be calculated on all data or only on selected regions (if any) ?
criteria:
should correlation coefficients be calculated from copy number ratios, or from smoothed copy number values given by GLAD ?
correlation:
which type of correlation coefficient should be used ?The Pearson correlation coefficient measures the extent to which the association between copy number and expression is linear; its sensitivity to outliers makes it suitable to detect associations within regions that are amplified in only few samples. The Spearman correlation coefficient is the Pearson coefficient between measurements ranks; it is therefore robust to outliers and able to detect non-linear associations


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Next: 3.3.11.2 Visualizing results Up: 3.3.11 Correlation Analysis Previous: 3.3.11 Correlation Analysis   Contents
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