Fit a repeated-measures model with dream

Fit a repeated-measures model with dream

Usage

de_dream(
  x,
  experiment,
  formula,
  assay = "counts",
  filter = TRUE,
  normalize_method = "TMM",
  contrast = NULL,
  ...
)

Arguments

x

A MultiAssayExperiment object.

experiment

Optional experiment name.

formula

Formula containing fixed and optional random effects.

assay

Assay name or one-based assay index.

filter

Remove low-expression features with edgeR::filterByExpr().

normalize_method

Library normalization method.

contrast

Optional contrast matrix passed as L to variancePartition::dream().

...

Additional arguments passed to variancePartition::dream().

Value

A native, empirical-Bayes moderated MArrayLM object.