Affymetrix analysis results in the generation of large and complex data sets which need extensive downstream analysis to determine results of biological significance. Users can benefit from a careful QC of their data before beginning analysis to remove individual chips that may adversely affect the final interpretation.

rptDB is a prototype database for the analysis of Affymetrix expression report (.rpt) files. Report files are widely used to QC raw data after hyb, scan and .cel file generation. Only %Present calls, Scale Factors and 3′:5′ ratios of housekeeping genes are generally used, but there are many other metrics that may also be of importance for QC analysis.

Authors: James Hadfield, Marielle Vigouroux
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