processAgilent {RCPA}

Process and normalize agilent-based dataset

Description

This function process TXT files and normalize expression data

Usage

processAgilent(dir, samples = NULL, greenOnly)

Arguments

dir

The path to the directory containing TXT files.

samples

A vector of samples IDs. If NULL, the function will automatically detect the samples in the directory.

greenOnly

Logical, for use with source, should the green (Cy3) channel only be read, or are both red and green required.

Details

Read and normalize expression data for agilent using limma normexp, loess, and quantile methods

Value

A matrix of normalized expression data. Rows are probes and columns are samples.

Examples

library(RCPA)
geoId <- "GSE28522"

downloadPath <- file.path(tempdir(), geoId)
fileList <- RCPA::downloadGEO(GEOID = geoId, protocol = "agilent",
                              platform ="GPL4133", destDir = downloadPath)

expression <- RCPA::processAgilent(downloadPath, greenOnly = FALSE)