Normalize SNP data using autosomes

Check this option to observations a two-step normalization on SNP intensity data:

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First, the observations from non-autosomes (X and Y) are separated from autosomes.

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The normalization is then applied only to autosome data.

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For each observation from non-autosomes, normalized data from the nearest smaller and nearest larger autosomes are interpolated.

Note: Checking this box disables the parameters corresponding to Baseline Reference for quantile normalization.

To Normalize SNP Data Using Autosomes:

8

Check the box.