rptDB; a prototype Affymetrix .rpt QC tool
Poster Sep 22, 2005
James Hadfield, Marielle Vigouroux
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.
When there is a need to quickly analyze samples using a number of different PCR assays, it is likely that optimal conditions for each assay will not be the same. First, different assays often will require different annealing temperatures for their primers. In addition, amplicons may be designed to be of different lengths and therefore require varying durations of the extension step.READ MORE