fit_lm: Run limma analysis.

In alexvpickering/crossmeta: Cross Platform Meta-Analysis of Microarray Data

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.

alexvpickering/crossmeta documentation built on May 23, 2024, 5:06 a.m.