Normalisation / Affymetrix SNP arrays

Description

Preprocesses Affymetrix SNP array CEL-files to give expression estimates and call values for genes.

Parameters

Details

Computes the genotype values using the SNPRMA and CRLMM methods.

100K and 500K SNP arrays can be analyzed. Currently, genome-wide arrays 5.0 or 6.0 are not supported.

Output

A tab-delimited text file containing gene names and expression estimates. This file is suitable for all further analyses.

References

This tool uses Bioconductor package oligo. You can cite the package as:

Benilton Carvalho, Henrik Bengtsson, Terence P Speed, and Rafael A Irizarry. Exploration, normalization, and genotype calls of high density oligonucleotide snp array data. Biostatistics, Dec 2006.