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AffyRNADegradation | Control and correction of RNA quality effects in GeneChip expression data

A package that assesses RNA quality of Affymetrix expression data. The AffyRNADegradation package extends the Bioconductor package affy and integrates well in a typical microarray analysis workflow. All calculations are performed directly on the AffyBatch object and carried out separately for each particular microarray hybridization in a single-chip approach. Our approach corrects the 3′/5′-bias on the level of raw probe intensities, which can afterward be processed with any method. The runtime is about 2 min and 3 min per sample for index and distance based corrections, respectively. Because each chip is processed independently, arbitrarily large data sets can be processed.

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AffyRNADegradation classification

AffyRNADegradation specifications

Unique identifier:
OMICS_01975
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

AffyRNADegradation distribution

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AffyRNADegradation support

Documentation

Credits

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Publications

Institution(s)

Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany

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