Introduction

MOTIVATION: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here. AVAILABILITY: The package is available via Bioconductor at the URL http://bioconductor.org/packages/release/bioc/html/AffyRNA Degradation.html

Publications

  1. AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
    Cite this
    Fasold M, Binder H, 2013-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Mario Fasold
    Developer

  2. Hans Binder
    Investigator

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Summary
AccessionBT006432
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByHans Binder