Matthew N McCall1, Harris A Jaffee, Rafael A Irizarry. 1. Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., CU 420630, Rochester, NY 14642, USA. mccallm@gmail.com
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.
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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