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

Matthew N. McCall | Zendy; Harris A. Jaffee | Zendy; Rafael A. Irizarry | Zendy

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

Author(s) -

Matthew N. McCall,

Harris A. Jaffee,

Rafael A. Irizarry

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts588

Subject(s) - bioconductor , preprocessor , computer science , software , r package , source code , exon , residual , algorithm , computational biology , artificial intelligence , gene , programming language , biology , genetics

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.

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