Method and apparatus for providing a bioinformatics database

• US 6,882,742 B2
• Filed: 02/25/2003
• Issued: 04/19/2005
• Est. Priority Date: 07/25/1997
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Balaban, David J., Aggarwal, Arun
• Primary Examiner(s): Mehta, Bhavesh M.
• Assistant Examiner(s): Choobin, Barry
• Application Number:
  US10/374,170
• Publication Number:
  US 20030125882A1
• Time in Patent Office: 784 Days
• Field of Search: 382/128, 382/274, 128/922, 250/455.11, 250/461.2, 435/4, 435/6, 356/39, 377/10, 377/13, 600/558, 702/19
• US Class Current: 382/128
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: H04M 1/006 Call diverting means
• CPC Class Codes: H04M 1/724 User interfaces specially adapted for cordless or mobile telephones
• CPC Class Codes: H04M 2207/206 composed of PSTN and wireless network
• CPC Class Codes: H04M 3/46 Arrangements for calling a number of substations in a predetermined sequence until an answer is obtained
• CPC Class Codes: H04M 3/54 Arrangements for diverting calls for one subscriber to another predetermined subscriber based on the calling party profile H04M3/42059; based on location H04M3/42348; based on presence H04M3/42365; to voice mail H04M3/53308
• CPC Class Codes: Y10S 128/922 including image analysis
• CPC Class Codes: Y10S 707/925 Drafting an application
• CPC Class Codes: Y10S 707/955 Object-oriented
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching
• CPC Class Codes: Y10S 707/99934 Query formulation, input preparation, or translation
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.

Claims

1. A computer-implemented method for analyzing a polymer probe array, the method comprising:

measuring a first plurality of intensities for a first plurality of picture elements respectively, the first plurality of picture elements corresponding to a first probe;

processing at least information associated with the first plurality of intensities;

determining a first average intensity associated with the first probe based on at least information associated with the first plurality of intensities; and

storing the first value of the first number of picture elements used to determine the first average intensity.

2. The method of claim 1, the method further comprising:

measuring a second plurality of intensities for a second plurality of picture elements respectively, the second plurality of picture elements corresponding to a second probe;

processing at least information associated with the second plurality of intensities;

determining a second average intensity associated with the second probe based on at least information associated with the second plurality of intensities; and

storing the second value of the second number of picture elements used to determine the second average intensity.

3. The method of claim 2, the method further comprising:

processing at least information associated with the first average intensity and the second average intensity;

determining consistency between at least the first average intensity and the second average intensity;

storing an indicator related to the consistency between at least the first average intensity and the second average intensity.

4. The method of claim 3, the method further comprising:

modifying the first average intensity;

storing the modified first average intensity;

storing the pre-modified first average intensity.

5. A computer-implemented method for analyzing information related to a polymer probe array including a plurality of probes, the method comprising:

measuring a first plurality of fluorescent intensities for a first plurality of picture elements respectively, the first plurality of picture elements associated with a first probe, the first probe related to a first location on a polymer probe array;

performing a first analysis on at least information associated with the first plurality of fluorescent intensities;

determining a first average intensity associated with the first probe based on at least information associated with the first plurality of fluorescent intensities;

obtaining a second average intensity associated with a second probe based on at least information associated with a second plurality of fluorescent intensities;

processing at least information associated with the first average intensity and the second average intensity;

storing the first average intensity associated with the first probe;

storing a first indicator related to a first type of the first analysis;

storing a first plurality of coordinates associated with the first location on the polymer probe array;

storing an indicator related to consistency or inconsistency between at least the first average intensity and the second average intensity.

6. The method of claim 5, the method further comprising:

determining a modified average intensity based on at least information associated with the first average intensity;

storing the modified average intensity.

7. The method of claim 5, the method further comprising:

processing information associated with the first plurality of fluorescent intensities;

determining a first standard deviation based on at least information associated with the first plurality of fluorescent intensities;

storing the first standard deviation.

8. The method of claim 5 wherein the obtaining a second average intensity comprises:

measuring the second plurality of fluorescent intensities for a second plurality of picture elements respectively, the second plurality of picture elements associated with the second probe, the second probe related to a second location on the polymer probe array;

performing a second analysis on at least information associated with the second plurality of fluorescent intensities;

determining the second average intensity associated with the second probe based on at least information associated with the second plurality of fluorescent intensities.

9. The method of claim 8 wherein the second analysis is associated with a second type, the second type being the same as the first type.

10. The method of claim 8 wherein the second analysis is associated with a second type, the second type being different from the first type.