Description

runs a differential expression analysis with Limma

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information. This can be used at the
workflow level to pass optional parameters to the module, e.g.
[ id:‘contrast1’, blocking:‘patient’ ] passed in as ext.args like:
‘—blocking_variable $meta.blocking’.

contrast_variable (string)

The column in the sample sheet that should be used to define groups for
comparison

reference (string)

The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples

target (string)

The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples

meta2 (map)

Groovy map containing study-wide metadata related to the sample sheet
and matrix

samplesheeet (file)

CSV or TSV format sample sheet with sample metadata

intensities (file)

Raw TSV or CSV format expression matrix with probes by row and samples
by column

Output

Name (Type)
Description
Pattern

results (file)

TSV-format table of differential expression information as output by Limma

*.limma.results.tsv

md_plot (file)

Limma mean difference plot

*.mean_difference.png

rdata (file)

Serialised MArrayLM object

*.MArrayLM.limma.rds

model (file)

TXT-format limma model

*.limma.model.tsv

session_info (file)

dump of R SessionInfo

*.log

versions (file)

File containing software versions

versions.yml