An application for assessing quality of RNA hybridized to Affymetrix GeneChips.
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.


BACKGROUND
The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm
Archer
Kellie J
KJ
Department of Biostatistics, Virginia Commonwealth University Richmond, VA 23298-0032, USA. kjarcher@vcu.edu
Guennel
Tobias
T
D000465:Algorithms; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D019544:Equipment Failure Analysis / Q000379:methods; D017403:In Situ Hybridization / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D011786:Quality Control; D012313:RNA / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
D015342:DNA Probes; D012313:RNA