In order to maximize confidence in gene fragment estimates using oligonucleotide microarrays such as the Affymetrix GeneChip , it’s necessary to identify arrays contaminated with artifacts not related to fragments of interest. While it is recognized that quality control measures should be implemented in generating gene expression data, existing quality control techniques employ limited functionality. One of the more critical metrics in assessing a genome chip is the overall chip brightness involving an estimate of the background noise on the chip. The overall chip brightness provides a basis for an automatic pass or fail. The quality metrics comprise a plurality of algorithms for detection of outliers resulting from commonly encountered defects.

The system for analyzing gene expression data obtained from a plurality of microarrays having mismatch (MM) probe pairs and perfect match (PM) probe pairs is automated. Image data for a plurality of scanned microarrays is stored in a database along with a set of microarray parameters which includes one or more image processing metrics for quality control of the microarray and a pass/fail status of the microarray as determined by these metrics. The user can search the database records according to one or more microarray parameters. The image processing metrics include algorithms for removing local background effects from the probe measurements by determining a model for estimated background using PM probe values.

A centralized application is provided for viewing, masking and pass/failing chips, and making use of the Image Processing (IP) metrics and limits. The application tracks the processes as a chip moves from registration and scan to publish and beyond. It permits users to view experiments, mask experiments if necessary, set pass/fail status and fail reason if fail, correct problems and view any of a number of chip parameters including IP (image processing) metrics and limits.

The Method and System for managing and querying gene expression data according to quality is covered by a patent in the name of Gene Logic. To know more about this patent, follow this link: http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=%22ocimum+biosolutions%22&OS=”ocimum+biosolutions”&RS=”ocimum+biosolutions“

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