processAffymetrix: Process and normalize affymetrix-based dataset

In RCPA: Consensus Pathway Analysis

Process and normalize affymetrix-based dataset

Description

This function process CEL files and normalize expression data

Usage

processAffymetrix(dir, samples = NULL)

Arguments

dir	The path to the directory containing CEL files.
samples	A vector of samples IDs. If NULL, the function will automatically detect the samples in the directory.

Details

Read and normalize expression data for affymetrix using RMA method

Value

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

Examples

library(RCPA)
geoId <- "GSE59761"
downloadPath <- file.path(tempdir(), geoId)
fileList <- RCPA::downloadGEO(GEOID = geoId, protocol = "affymetrix",
                               platform ="GPL16311", destDir = downloadPath)
# process only 3 samples
expression <- RCPA::processAffymetrix(downloadPath, 
                   samples = c("GSM1446171", "GSM1446172", "GSM1446173"))

RCPA documentation built on May 29, 2024, 4:24 a.m.