preprocessCELFiles: RMA preprocess CEL files

In AEBilgrau/DLBCLdata: Automated and reproducible download and preprocessing of DLBCL data

Description

General function for RMA processing microarray data. Automatically downloads custom Brainarray chip definition files (cdf) if wanted.

Usage

preprocessCELFiles(cel_files, cdf = c("affy", "brainarray"), target,
  version = getLatestVersion(), background = TRUE, normalize = TRUE)

Arguments

cel_files	A character vector of .CEL files.
cdf	A character specifying the CDF type to use. Should be either "brainarray" or "affy".
target	Specifies the "target" CDF to use depending on cdf. If cdf is "affy" then target is e.g. "core". If cdf is "brainarray" then target is e.g. "ensg", "entrez". See listTargets() to list the available targets.
version	A character giving the brainarray version to be used. Only used if cdf is "brainarray". See listVersions().
background	boolean. Should RMA background correction be performed?
normalize	boolean. Should RMA normalization be performed?

Value

An expression set object.

AEBilgrau/DLBCLdata documentation built on May 5, 2019, 11:29 a.m.