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Why does the normalization subtract off SNP means? Wouldn it be theoretically correct to subtract off sample means instead?

April 26, 2017means Normalization sample SNP subtract theoretically

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Why does the normalization subtract off SNP means? Wouldn it be theoretically correct to subtract off sample means instead?

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The decision to subtract off SNP means instead of sample means was an empirical choice to ensure that results are invariant to flipping the SNP alleles (i.e. changing 0/1/2 to 2/1/0).