BACKGROUND: Used alone, the MAS5.0 algorithm for generating expression summaries has been criticized for high False Positive rates resulting from exaggerated variance at low intensities. RESULTS: Here we show, with replicated cell line data, that, when used alongside detection calls, MAS5 can be both selective and sensitive. A set of differentially expressed transcripts were identified that were found to be changing by MAS5, but unchanging by RMA and GCRMA. Subsequent analysis by real time PCR confirmed these changes. In addition, with the Latin square datasets often used to assess expression summary algorithms, filtered MAS5.0 was found to have performance approaching that of its peers. CONCLUSION: When used alongside detection calls, MAS5 is a sensitive and selective algorithm for identifying differentially expressed genes.

UNLABELLED: ADAPT is an online database providing comprehensive mappings between Affymetrix probes and RefSeq and Ensembl transcripts. ADAPT was designed to help interpret microarray experiments by providing a means to explore the many-to-many relationships that exist between probes, probesets, transcripts and genes. AVAILABILITY: ADAPT can be queried via the web at http://bioinformatics.picr.man.ac.uk/adapt

UNLABELLED: Quality Control is a fundamental aspect of successful microarray data analysis. Simpleaffy is a BioConductor package that provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls. AVAILABILITY: Simpleaffy can be downloaded from http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional information can be found on the supplementary website located at http://bioinformatics.picr.man.ac.uk.