oligo-package {oligo}R Documentation

The oligo package: a tool for analysis of oligonucleotide arrays

Description

The oligo package handles oligonucleotide arrays: expression, tiling, SNP and exon chips. The supported manufacturers are Affymetrix and NimbleGen. The package provides tools for preprocessing.

Details

The package will read the raw intensity files (CEL for Affymetrix; XYS for NimbleGen) and allow the user to perform analyses starting at the feature-level.

Reading in the intensity files require the existence of data packages that contain the chip specific information (X/Y coordinates; feature types; sequence). These data packages packages are build using the makePlatformDesign package, except for the Affymetrix SNP arrays that uses the data packages built via pdInfoBuilder package. Soon, all the data packages will be built using the pdInfoBuilder package.

Author(s)

Benilton Carvalho - bcarvalh@jhsph.edu

References

Carvalho, B.; Bengtsson, H.; Speed, T. P. & Irizarry, R. A. Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data. Biostatistics, 2006.

Examples

## rawData <- read.celfiles(list.celfiles())
## preProc <- snprma(rawData)
## gtCalls <- crlmm(preProc, correctionFile="outEM.rda")

[Package oligo version 1.0.2-6 Index]