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Feature extraction software automatically flagged non-uniform features and population outliers, considering acceptable outlier numbers lower than 5% of total feature number on the array.
The MDS plot shows that Malagasy Y chromosome lineages are an outlier to Indonesian populations, in a similar way to certain Indonesian population outliers (Mentawai, Nias, Besemah, Semende).
Population outliers were excluded when averaging replicated probes.
Principal component analysis did not reveal any population stratification or population outliers (Figure S1).
Assessment for population outliers identified 12 subjects displaying significantly different allele frequencies than the remainder of the population.
After data cleaning followed by principal components analysis to remove population outliers [6], this dataset comprised 1618 MS cases of European ancestry from Australia and New Zealand, and 3413 European-ancestry controls from Australia, the UK and US.
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All control spots, non-uniform spots and population outlier spots were removed from the dataset; intensity values were log transformed using AgilentFilter, software designed to simplify the processing of Agilent data.
As the Bayescan analysis required combining populations, outlier loci could not be attributed to a specific hatchery line.
Features on the array that were flagged as "Population outlier" or "Non-uniformity outlier" were removed from the data and not considered further.
Whiskers in the boxplots represent the range of the minimum and maximum alpha diversity values within a population, excluding outliers.
Eigenstrat [ 18] was run on a pruned SNP set with default settings to exclude population ancestry outliers and ensure cases and controls were ethnically matched.
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