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AU2001257114A1 - Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data - Google Patents

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

Info

Publication number
AU2001257114A1
AU2001257114A1 AU2001257114A AU5711401A AU2001257114A1 AU 2001257114 A1 AU2001257114 A1 AU 2001257114A1 AU 2001257114 A AU2001257114 A AU 2001257114A AU 5711401 A AU5711401 A AU 5711401A AU 2001257114 A1 AU2001257114 A1 AU 2001257114A1
Authority
AU
Australia
Prior art keywords
gene expression
feature extraction
array data
density oligonucleotide
expression array
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
AU2001257114A
Inventor
Li Cheng
Wing Hung Wong
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of California San Diego UCSD
Original Assignee
University of California
University of California Berkeley
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by University of California, University of California Berkeley filed Critical University of California
Publication of AU2001257114A1 publication Critical patent/AU2001257114A1/en
Abandoned legal-status Critical Current

Links

Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y15/00—Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00—Image analysis
    • G06T7/0002—Inspection of images, e.g. flaw detection
    • G06T7/0012—Biomedical image inspection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00—Indexing scheme for image analysis or image enhancement
    • G06T2207/30—Subject of image; Context of image processing
    • G06T2207/30004—Biomedical image processing
    • G06T2207/30068—Mammography; Breast

Landscapes

  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Nanotechnology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Radiology & Medical Imaging (AREA)
  • Quality & Reliability (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • General Physics & Mathematics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
AU2001257114A 2000-04-21 2001-04-20 Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data Abandoned AU2001257114A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US09/556,497 2000-04-21
US09/556,497 US6571005B1 (en) 2000-04-21 2000-04-21 Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
PCT/US2001/012748 WO2001081542A2 (en) 2000-04-21 2001-04-20 Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

Publications (1)

Publication Number Publication Date
AU2001257114A1 true AU2001257114A1 (en) 2001-11-07

Family

ID=24221578

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2001257114A Abandoned AU2001257114A1 (en) 2000-04-21 2001-04-20 Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

Country Status (3)

Country Link
US (2) US6571005B1 (en)
AU (1) AU2001257114A1 (en)
WO (1) WO2001081542A2 (en)

Families Citing this family (33)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6090555A (en) * 1997-12-11 2000-07-18 Affymetrix, Inc. Scanned image alignment systems and methods
US5631734A (en) 1994-02-10 1997-05-20 Affymetrix, Inc. Method and apparatus for detection of fluorescently labeled materials
US6741344B1 (en) * 1994-02-10 2004-05-25 Affymetrix, Inc. Method and apparatus for detection of fluorescently labeled materials
US6591196B1 (en) * 2000-06-06 2003-07-08 Agilent Technologies Inc. Method and system for extracting data from surface array deposited features
DE60124598T2 (en) * 2000-06-06 2007-09-06 Agilent Technologies, Inc., Palo Alto Method and system for determining the orientation of a microarray
US7062092B2 (en) 2000-08-22 2006-06-13 Affymetrix, Inc. System, method, and computer software product for gain adjustment in biological microarray scanner
US6829376B2 (en) * 2000-10-24 2004-12-07 Affymetrix, Inc. Computer software system, method, and product for scanned image alignment
US7130458B2 (en) * 2000-10-24 2006-10-31 Affymetrix, Inc. Computer software system, method, and product for scanned image alignment
IL141151A0 (en) * 2001-01-29 2002-02-10 Compugen Ltd Method for comparing signal arrays in digital images
WO2003033128A2 (en) * 2001-10-12 2003-04-24 Duke University Methods for image analysis of high-density synthetic dna microarrays
US20030143551A1 (en) * 2002-01-30 2003-07-31 Cattell Herbert F. Reading multiple chemical arrays
US20040072191A1 (en) * 2002-03-07 2004-04-15 Alex Chenchik Antisense RNA standardizing control
US20040006431A1 (en) * 2002-03-21 2004-01-08 Affymetrix, Inc., A Corporation Organized Under The Laws Of Delaware System, method and computer software product for grid placement, alignment and analysis of images of biological probe arrays
WO2003093810A1 (en) * 2002-05-03 2003-11-13 Vialogy Corporation System and method for characterizing microarray output data
US20030216870A1 (en) * 2002-05-07 2003-11-20 Wolber Paul K. Method and system for normalization of micro array data based on local normalization of rank-ordered, globally normalized data
US20030220746A1 (en) * 2002-05-21 2003-11-27 Srinka Ghosh Method and system for computing and applying a global, multi-channel background correction to a feature-based data set obtained from scanning a molecular array
JP2004118154A (en) * 2002-09-30 2004-04-15 Canon Inc Belt conveying device and image forming device
US20040243341A1 (en) * 2003-05-30 2004-12-02 Le Cocq Christian A. Feature extraction methods and systems
US7324677B2 (en) * 2003-10-14 2008-01-29 Agilent Technologies, Inc. Feature quantitation methods and system
US7302348B2 (en) 2004-06-02 2007-11-27 Agilent Technologies, Inc. Method and system for quantifying and removing spatial-intensity trends in microarray data
US20060040287A1 (en) * 2004-06-02 2006-02-23 Corson John F Method and system for quantifying random errors and any spatial-intensity trends present in microarray data sets
US20050281462A1 (en) * 2004-06-16 2005-12-22 Jayati Ghosh System and method of automated processing of multiple microarray images
US7877213B2 (en) 2004-09-23 2011-01-25 Agilent Technologies, Inc. System and methods for automated processing of multiple chemical arrays
US8173367B2 (en) * 2004-10-18 2012-05-08 Sherri Boucher In situ dilution of external controls for use in microarrays
US7480593B2 (en) * 2005-08-03 2009-01-20 Suresh Gopalan Methods and systems for high confidence utilization of datasets
US20070154923A1 (en) * 2005-12-29 2007-07-05 Affymetrix, Inc. Method for Gridding and Quality Control of Polymer Arrays
US8055098B2 (en) * 2006-01-27 2011-11-08 Affymetrix, Inc. System, method, and product for imaging probe arrays with small feature sizes
US9445025B2 (en) 2006-01-27 2016-09-13 Affymetrix, Inc. System, method, and product for imaging probe arrays with small feature sizes
US8009889B2 (en) * 2006-06-27 2011-08-30 Affymetrix, Inc. Feature intensity reconstruction of biological probe array
US8010307B2 (en) * 2006-12-07 2011-08-30 Hermes-Microvision, Inc. In-line overlay measurement using charged particle beam system
US20080175468A1 (en) * 2007-01-24 2008-07-24 Hermes Microvision, Inc. Method and system for creating knowledge and selecting features in a semiconductor device
FI20085302A0 (en) * 2008-04-10 2008-04-10 Valtion Teknillinen Correction of measurements of biological signals from parallel measuring devices
US9378549B2 (en) * 2013-03-05 2016-06-28 Kabushiki Kaisha Toshiba Estimation of confidence limits for measurements derived from image data

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6040138A (en) * 1995-09-15 2000-03-21 Affymetrix, Inc. Expression monitoring by hybridization to high density oligonucleotide arrays
US5744101A (en) * 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US6027880A (en) * 1995-08-02 2000-02-22 Affymetrix, Inc. Arrays of nucleic acid probes and methods of using the same for detecting cystic fibrosis
US5790692A (en) * 1994-09-07 1998-08-04 Jeffrey H. Price Method and means of least squares designed filters for image segmentation in scanning cytometry
GB2294319B (en) * 1994-10-20 1999-06-16 Cambridge Imaging Ltd Improved imaging method and apparatus
US6156502A (en) * 1995-12-21 2000-12-05 Beattie; Kenneth Loren Arbitrary sequence oligonucleotide fingerprinting
US6007994A (en) * 1995-12-22 1999-12-28 Yale University Multiparametric fluorescence in situ hybridization
US6225086B1 (en) * 1997-05-21 2001-05-01 Yale University Polynucleotides encoding ankyrin proteins
CA2307674C (en) * 1997-10-30 2013-02-05 Cold Spring Harbor Laboratory Probe arrays and methods of using probe arrays for distinguishing dna
US6171793B1 (en) * 1999-04-19 2001-01-09 Affymetrix, Inc. Method for scanning gene probe array to produce data having dynamic range that exceeds that of scanner

Also Published As

Publication number Publication date
US6571005B1 (en) 2003-05-27
WO2001081542A2 (en) 2001-11-01
US20040033485A1 (en) 2004-02-19
WO2001081542A3 (en) 2002-03-07
WO2001081542A9 (en) 2003-01-16

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