AffyRNADegradation

The "AffyRNADegradation" R package addresses the issue of RNA degradation in gene expression experiments, particularly those utilizing Affymetrix expression arrays. Given that RNA quality can significantly impact the accuracy of transcript quantification due to degradation and variations in amplification efficiency, tools to assess and correct for these factors are crucial.

This package introduces a novel approach by analyzing the positional intensity decay of probes on the transcript, offering an estimate of RNA quality within a sample. Moreover, it adjusts probe intensities to compensate for any identified degradation bias. Prior to this development, no software solution was available that could perform these specific tasks.

The introduction of "AffyRNADegradation" fills a significant gap in the preprocessing of Affymetrix array data, enabling researchers to improve the reliability of gene expression measurements. By providing a means to assess RNA degradation directly from array data and adjust intensities accordingly, this package enhances the accuracy of gene expression analysis, thus facilitating more robust biological interpretations and findings.