merge_experiments.ExpressionSet: Rough merger of microarray experiments

In madhulika-EBI/Batchevaluation: Toolkit for batch correction

Rough merger of microarray experiments

Description

The function merge_experiments merges all the experiments in the list in a single experiment object and doesn't perform any correction. This function has two additional arguments log and filter (set to TRUE by default). It is recommended to give microarray data only with back-ground correction and after filtering low-expressed genes

Usage

merge_experiment.ExpressionSet(
  experiments,
  filter.unexpressed.genes = TRUE,
  log,
  force = FALSE
)

Arguments

experiments	A list of wrapped experiments.
filter.unexpressed.genes	A logical indicating if the genes that are unexpressed across all the samples of a batch shall be removed. This is for the proper functioning of the current version of ComBat in correct_batch_effect.
log	A logical ndicating of whether the data shall be log-transformed(recommended).
force	A logical. If the experiments of the list are of different classes, the function is stopped, unless force=TRUE.

Value

Single ExpressionSet

Note

Caution: Sometime during merging experiments, phenodata (SDRF) file gets corrupted, it is advised to always check meta-data before proceeding further.

madhulika-EBI/Batchevaluation documentation built on Jan. 27, 2023, 5:27 p.m.