BackgroundSubtraction: Perform background subtraction on normalized data

In TomNash/NASHMAP: Microarray Analysis Pipeline

Description

Remove all genes that have an maximum intensity level below that of the provided cutoff.

Usage

BackgroundSubtraction(preprocess.data.obj, 
method=c("mloess", "quantile"), cutoff)

Arguments

preprocess.data.obj	Object returned from call to preprocess.data
method	Type of normalization to use: "quantile" for quantile normalization; "mloess" for MLOESS normalization; "raw" for raw data
cutoff	The cutoff value (binary logarithm) identified through background.cutoff

Value

A list with components

ntext	Number of leading text columns
data.col	Vector of column indices containing array data
id	Vector containing gene ID's
symbol	Vector containing gene symbols
desc.stats	Vector of column indices containing descriptive statistics
pipeline.name	Name of pipeline generated from input file name sans extension
normalized	Data frame of descriptive stats and normalized data for the chosen method

TomNash/NASHMAP documentation built on May 9, 2019, 4:54 p.m.