1
Jayati Ghosh, Bill J Peck, Eric M Leproust, Charles David Troup, Glenda Choate Delenstarr, Patrick J Collins, John F Corson, Paul K Wolber, Xiangyang Zhou: Method and system for quantifying and removing spatial-intensity trends in microarray data. Agilent Technologies, November 27, 2007: US07302348 (56 worldwide citation)

A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the sel ...


2
John F Corson, Debra A Sillman, Jayati Ghosh, Kenneth L Staton: Signal offset for prevention of data clipping in a molecular array scanner. Agilent Technologies, July 5, 2005: US06914229 (13 worldwide citation)

A method and system for preventing signal clipping in a molecular array scanner by adding an offset signal to the signal generated by the photodetectors and initial stages of signal processing within a molecular array scanner in order to promote the signal above the level where signal information is ...


3
Jayati Ghosh, John F Corson, Debra A Sillman: Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners. Agilent Technologies, December 28, 2004: US06835938 (13 worldwide citation)

A method and system for determining a biopolymer array substrate thickness dependent optimal focus distance for scanning a molecular array by a molecular array scanner are disclosed. Also disclosed are methods of determining the thickness of a biopolymer array substrate using a position sensitive de ...


4
Jayati Ghosh, John F Corson, Debra A Sillman: Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners. Agilent Technologies, April 22, 2008: US07361906 (10 worldwide citation)

A method and system for determining a biopolymer array substrate thickness dependent optimal focus distance for scanning a molecular array by a molecular array scanner are provided. A reference substrate is automatically scanned at successively greater distances of the stage from a light gathering m ...


5
Bo U Curry, Andreas N Dorsel, Jayati Ghosh, Kenneth L Staton: Method for improved focus control in molecular array scanning by using a symmetrical filter to determine in-focus-distance. Agilent Technologies, June 27, 2006: US07067783 (6 worldwide citation)

Automated methods and systems for determining an in-focus-distance for a position on the surface of a molecular array substrate using a molecular array scanner are provided. A signal from a first position of an array substrate is detected and noise is filtered out of the detected signal using a symm ...


6
John Frederick Corson, Jayati Ghosh, Svetlana Shchegrova: Methods and systems for detrending signal intensity data from chemical arrays. Agilent Technologies, October 14, 2008: US07437249 (4 worldwide citation)

Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the s ...


7
Bo U Curry, Jayati Ghosh, Kenneth L Staton: Bi-directional scanner control system. Agilent Technologies, August 9, 2005: US06927389 (4 worldwide citation)

Optical scanner system approaches are described in which novel focusing approaches are provided. A control algorithm accounts for geometric variation of successive scans in opposite directions across a microarray slide or substrate in order to provide optimized focus. The feedback approach taught ma ...


8
Glenda C Delenstarr, Jayati Ghosh, John F Corson: System and methods for characterization of chemical arrays for quality control. Agilent Technologies, February 19, 2008: US07333907 (3 worldwide citation)

Systems, methods and computer readable media for characterizing a chemical array. At least one metric indicative of accuracy of location of features on the chemical array by a feature extraction process used to extract signals from features of the chemical array may be generated, as well as addition ...


9
Debra Ann Sillman, Xiangyang Zhou, Chetan D Jadhaw, Herbert F Cattell, Jayati Ghosh: Scanning parameterization for biopolymeric array scanner. Agilent Technologies, July 5, 2005: US06913200 (2 worldwide citation)

Methods for programming an array scanner to scan a plurality of biopolymer arrays are provided. In the subject methods, individual scanning parameters for at least two different arrays of the plurality of arrays to be scanned are selected and input into the array scanner prior to scanning the plural ...


10
Jayati Ghosh, Amir Ben dor, Anya Tsalenko, Bo Curry: Method and system for analysis of array-based, comparative-hybridization data. Agilent Technologies, February 9, 2010: US07660675 (1 worldwide citation)

Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.