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]