RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: Release (2.11)

A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

Author: Nusrat Rabbee <nrabbee at post.harvard.edu>, Gary Wong <wongg62 at berkeley.edu>

Maintainer: Nusrat Rabbee <nrabbee at post.harvard.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("RLMM")

To cite this package in a publication, start R and enter:

    citation("RLMM")

Documentation

Details

Package Downloads