process_eset: Processing of expression data

Description Usage Arguments Details Value Author(s)

View source: R/GEX_process_eset.R

Description

Normalisation, transformation and/or probe quality filtering of expression data.

Usage

1
process_eset(eset, method_norm = "quantile", transform = "none")

Arguments

eset

ExpressionSet or ExpressionSetIllumina

method_norm

character with normalisation method. Options are "quantile", "qspline", "vsn", "rankInvariant", "median" and "none"

transform

character with data transformation method. Options are "none", "log2", "neqc", "rsn" and "vst".

Details

Expression data is normalised and/or transformed by algorithms dedicated in 'method_norm' and/or 'transform'. If a column PROBEQUALITY is available within the feature data as for Illumina expression arrays, probes assigned a ‘Bad’ or ‘No match’ quality score after normalisiation are removed from the dataset. Lastly, if the input object is of class ExpressionSetIllumina, it is changed to ExpressionSet to avoid later incompabilities with the 'limma'-package.

Value

processed ExpressionSet object

Author(s)

Frank Ruehle


frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.