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Chunk #57 — Online Methods — Generate data-driven covariance matrices Uk.

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Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.
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In addition to the covariance matrices obtained from this EM algorithm, we define more covariance matrices from the SFA results; specifically, the Q = 5 rank-1 matrices FqTLqTLqFq, with q = 1,…,Q. The rationale for adding these rank-1 covariance matrices is that the SFA factors may directly reflect effect patterns in the data, and if so these matrices will be a helpful addition. (If they are not helpful, they will receive little weight when estimating π).