An application for assessing quality of RNA hybridized to Affymetrix GeneChips.
basic_science · Level V
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- Record sourced from PubMed, PMID 16935927.
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Abstract
This paper describes a stand-alone application for estimating the 3' to 5' ratio by fitting a mixed effects model to the interior pixel intensities of perfect match probes for selected control probe sets from an Affymetrix *.DAT file. The effectiveness of this method was demonstrated previously by an application of the method to two microarray datasets for which external verification of RNA quality was known. This application provides a more objective assessment of sample quality in that both a point estimate and 95% confidence interval about the 3' to 5' ratio are provided. The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm
Medical subject headings
- DNA Probes
- In Situ Hybridization
- Oligonucleotide Array Sequence Analysis
- RNA
- Sequence Analysis, DNA
- Software