fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

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Abstract

Summary:

Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms—Affymetrix Human Exon and Gene 1.0 ST—by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects.

Availability and implementation:

All packages are implemented in R. Source code and binaries are freely available through the Bioconductor project. Convenient links to all software and data packages can be found at http://mnmccall.com/software

Contact:

mccallm@gmail.com

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