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The generation of SWIFT cluster templates and their use in sample comparisons are demonstrated in Tutorial 3 (see Supporting Information).
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All pairwise population sample comparisons were replicated with different random number seeds.
The P Test significance (p-values) for each pair of sample comparisons was obtained using 1,000 permutations.
P values for tumor growth were calculated by Kaplan-Meier Time to Progression method, and p values for two sample comparisons were calculated by two-sided Wilcoxon Rank-Sum test.
Two sample comparisons were done by paired sample t test.
Sample comparisons were done by the Chi-Square Test.
Both clustering and sample comparisons were performed using Agilent GeneSpring software12.5 (Agilent Technologies; Palo Alto, CA).
Final sample comparisons were expressed as units per milligram of total protein.
Analysis of variance against all pairwise sample comparisons was performed with a 5% false discovery rate (FDR).
Both fold change and p value for pairwise sample comparisons were calculated for evaluating differentially expressed genes.
A similar series of Bonferroni adjusted two sample comparisons were conducted for Year 2 (i.e. gender and year of entry to programme).
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