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The shrinkage t statistics calculated from the permutations were pooled across genes that are not significant [15] at nominal 0.1 level according to a conservative gene specific t test to form one overall empirical distribution.
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For this permutation test, the subgenomes (XLMR and non-XLMR subgenomes) were pooled together and then divided into nonoverlapping 2 kb fragments.
Since the permutation samples are pooled across all replicates to form a sample from the null, B can be set to be much smaller than the situation when only one sample is analyzed.
They also propose two STs based on a bootstrap and permutation resampling approach where the data are pooled across all antigens.
Five thousand permutations were run.
One thousand permutations were used.
One hundred thousand permutations were used.
A total of 1000 permutations were performed.
1000 random permutations were used.
1000 permutations were used for each process.
A number of 10,000,000 permutations were replicated.
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