Agilent Technologies, Inc.

Ciphergen Biosystems, Inc.

Cynthia Y Enderwick

Nicholas Michael Sampas

Paul K Wolber

Glenda Choate Delenstarr

Zohar H Yakhini

Herbert F Cattell

Edward J Gavin

Patrick Ho

Scott D Connell

Niels Kirk Thomsen

A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Method and system for extracting data from surface array deposited features

A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

One embodiment of the invention is directed to a method of processing a plurality of spectra. The method includes receiving values associated with a plurality of sample spots on one or more sample chips, wherein the values were entered using graphic elements representing the sample spots, the graphic elements being displayed on a graphical user interface. Data representing a plurality of signals are received. Each signal in the plurality of signals is annotated with a set of values associated with the sample spot from which the signal is generated.

Data management system and method for processing signals from sample spots

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San Jose, CA, United States of America

Cynthia Y Enderwick