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Probe region expression estimation for RNA-seq data for improved microarray comparability

Bioconductor version: 2.13

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

Author: Karolis Uziela and Antti Honkela

Maintainer: Karolis Uziela <karolis.uziela at>

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PDF R Script prebs User Guide
PDF   Reference Manual


biocViews Bioinformatics, GeneExpression, Microarray, Preprocessing, RNAseq, Sequencing, Software
Version 1.2.1
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends R (>= 2.14.0), Rsamtools(>= 1.13.1), affy
Imports parallel, methods, stats, GenomicRanges(>= 1.13.3), IRanges
Suggests prebsdata, hgu133plus2cdf, hgu133plus2probe
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