fit_lm {crossmeta} | R Documentation

## Run limma analysis.

### Description

Runs limma differential expression analysis on all contrasts selected by `add_contrast`. Analysis performed with and without surrogate variables discovered by `diff_setup`. Also prints MDS plot and saves results.

### Usage

    fit_lm(eset, svobj = list(sv = NULL), numsv = 0, rna_seq = TRUE)

### Arguments

`eset` | Annotated eset created by `load_raw`. Replicate features and non-selected samples removed by `iqr_replicates`.
`svobj` | Surrogate variable analysis results. Returned from run_sva.
`numsv` | Number of surrogate variables to model.
`rna_seq` | Is this an RNA-seq `eset`? Default is `TRUE`.

### Value

list with slots: * `fit` Result of lmFit. * `mod` model matrix used for fit.

[Package crossmeta version 1.20.0 Index]