Method and apparatus for providing a bioinformatics database

• US 7,215,804 B2
• Filed: 03/14/2005
• Issued: 05/08/2007
• Est. Priority Date: 07/25/1997
• Status: Expired due to Fees

• 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): Dang; Duy M.
• Application Number:
  US11/080,216
• Publication Number:
  US 20050157915A1
• Time in Patent Office: 785 Days
• Field of Search: 382/129, 382/128, 382/271, 382/274, 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 showing a result of an analysis of a polymer probe array including multiple probes, said method comprising the steps of:

determining an average fluorescent intensity for a given probe as values of a plurality of picture elements; and

storing the value of the number of picture elements used to determine the average fluorescent intensity for the given probe.

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

modifying the average fluorescent intensity;

storing the modified fluorescent average intensity.

3. The method of claim 2, and further comprising storing the pre-modifled average fluorescent intensity.

4. The method of claim 1 wherein the determining an average fluorescent intensity comprises determining an average fluorescent intensity based on at least information associated with a plurality of fluorescent intensities.

5. The method of claim 4, and further comprising:

processing information associated with the plurality of fluorescent intensities;

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

storing the standard deviation.