Description Usage Arguments Value Author(s) References See Also
Modified (slimmed down) version of limma's eBayes, which uses a shrinkage approach to moderate t statistics from tests for differential expression across the genome.
1 |
fit |
list with elements $sigma, $df.residual, $Amean (if trend=TRUE), $coefficients, and $stdev.unscaled. Usually the output of getLimmaInput (the $ebobject item), a more memory-efficient version of lmFit. |
trend |
as in eBayes, if TRUE, allow an intensity trend in the priors of variances (across genes/bps) |
A list with elements
tt |
moderated t statistics for each gene/bp |
logfchange |
estimated log2 fold change on coverage between the groups, as estimated by a linear model |
Alyssa Frazee
Smyth G (2004). "Linear models and empirical Bayes methods for assessing differential expression in microarray experiments." Statistical Applications in Genetics and Molecular Biology 3(1): Article 3.
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