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A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: Release (3.1)

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>, Gary Wong <wongg62 at>

Maintainer: Nusrat Rabbee <nrabbee at>

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PDF R Script RLMM Doc
PDF   Reference Manual


biocViews GeneticVariability, Microarray, OneChannel, SNP, Software
Version 1.30.0
In Bioconductor since BioC 1.8 (R-2.3) (9.5 years)
License LGPL (>= 2)
Depends R (>= 2.1.0)
Imports graphics, grDevices, MASS, stats, utils
SystemRequirements Internal files Xba.CQV, Xba.regions (or other regions file)
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