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Sample populations were compared either pair wise using the Mann-Whitney U test or in groups of more than two using the Kruskal-Wallis test.
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Probability maps of cerebral infarction were rendered group-wise using the individual segmentation results of each animal.
Ion chromatograms were compared pair-wise using the SIEVE software (Thermo Scientific).
The genomes of CP220 and CPt10 were compared pair-wise using the Artemis Comparison Tool (ACT) [ 42].
To remove redundancy, EST sequences were assembled into contigs and singlets, species-wise, using the sequence assembly program CAP3 with its default setting [ 67].
Therefore, the data were normalised SNP-wise using the mean and s.d. of the germline samples, that is, z ij =(x ij −mean j )/s.d.d
Missing data were imputed instrument-wise, using the SPSS Missing Value Analysis (MVA), Expectation Maximization (EM), for respondents with valid data for at least half the items of each instrument.
Next, ratios were computed from the log-ratios and quantile-normalized (experiment-wise) using the normalizeQuantile function from the R package [ 70], so that all experiments had the same average sample distribution.
The fitting of all spectra was done with mixed Gaussian Lorentzians, unless other wise stated, using the Casa XPS program.
Tests with significant F ratios were analyzed for significance using post hoc pair wise comparisons using the Bonferroni adjustment.
Ks and Ka values were calculated in a pair wise model using the CODEML program in the PAML package version 4.4 [ 68].
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