SYSTEM, METHOD, AND COMPUTER PRODUCT FOR CORRECTION OF FEATURE OVERLAP

• US 20060293860A1
• Filed: 06/28/2006
• Published: 12/28/2006
• Est. Priority Date: 06/28/2005
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Bressler, Vincent E., Stern, David, Bukys, Albert K.
• Application Number:
  US11/427,103
• Publication Number:
  US 20060293860A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

In one embodiment, a method for correcting feature overlap in biological probe array data is described that comprises (a) receiving a first set of data comprising an intensity value for each of a plurality of features associated with a probe array; (b) calculating a crosstalk parameter for the first set of data using the intensity values of one or more test features and a plurality of features that neighbor each test feature; and (c) applying the crosstalk parameter to each intensity value in the first set of data to produce a second set of data.

Claims

1. A method for correcting feature overlap in biological probe array data, comprising:

(a) receiving a first set of data comprising an intensity value for each of a plurality of features associated with a probe array;

(b) calculating a crosstalk parameter for the first set of data using the intensity values of one or more test features and a plurality of features that neighbor each test feature; and

(c) applying the crosstalk parameter to each intensity value in the first set of data to produce a second set of data.

2. The method of claim 1, wherein:

at least one of the plurality of features comprise probe features.

3. The method of claim 1, wherein:

at least one of the plurality of features comprise control features.

4. The method of claim 1, wherein:

the first set of data is generated by processing raw data from a scanned biological probe array.

5. The method of claim 4, wherein:

the first set of data is a .cel file.

6. The method of claim 1, wherein:

the crosstalk parameter represents a measure of feature leakage.

7. The method of claim 6, wherein:

feature leakage includes an intensity contribution from a first feature to one or more neighboring features.

8. The method of claim 6, wherein:

feature leakage is the result of blurring.

9. The method of claim 8, wherein:

the blurring is associated with a point spread function of an optical instrument.

10. The method of claim 8, wherein:

a source of the blurring includes one or more of the group consisting of diffraction, spherical aberration, coma, defocus, vibration, turbulence in the air or liquid between the imaged object and the lens element, and temperature differences.

11. The method of claim 1, further comprising:

applying steps (b)-(c) for a plurality of sub-sets of the set of data

12. The method of claim 11, wherein:

the sub-sets are associated with regions in an image

13. A system for correcting feature overlap in biological probe array data, comprising:

a input manager that receives a first set of data comprising an intensity value for each of a plurality of features associated with a probe array;

a calculator that calculates a crosstalk parameter for the first set of data using the intensity values of one or more test features and a plurality of features that neighbor each test feature; and

an adjuster that applies the crosstalk parameter to each intensity value in the first set of data to produce a second set of data.

14. The system of claim 13, wherein:

at least one of the plurality of features comprise probe features.

15. The system of claim 13, wherein:

at least one of the plurality of features comprise control features.

16. The system of claim 13, wherein:

the first set of data is generated by processing raw data from a scanned biological probe array.

17. The system of claim 16, wherein:

the first set of data is a .cel file.

18. The system of claim 13, wherein:

the crosstalk parameter represents a measure of feature leakage.

19. The system of claim 18, wherein:

feature leakage includes an intensity contribution from a first feature to one or more neighboring features.

20. The system of claim 18, wherein:

feature leakage is the result of blurring.

21. The system of claim 20, wherein:

the blurring is associated with a point spread function of an optical instrument.

22. The method of claim 20, wherein:

a source of the blurring includes one or more of the group consisting of diffraction, spherical aberration, coma, defocus, vibration, turbulence in the air or liquid between the imaged object and the lens element, and temperature differences.

23. The system of claim 13, wherein:

the calculator calculates a crosstalk parameter for each of a plurality of sub-sets of the set of data; and

the adjuster applies each crosstalk parameter to each intensity value in the associated sub-set.

24. The system of claim 23, wherein:

the sub-sets are associated with regions in an image

25. A system for correcting feature overlap in biological probe array data, comprising:

a scanner that acquires a first set of data from a biological probe array; and

a computer comprising executable code stored thereon, wherein the executable code performs a method of;

processing the first set of data to produce a second set of data comprising an intensity value for each of a plurality of features associated with the probe array;

calculating a crosstalk parameter for the second set of data using the intensity values of one or more test features and one or more features that neighbor each test feature; and

applying the crosstalk parameter to each intensity value in the second set of data to produce a third set of data.

26. A method for correcting feature overlap in biological probe array data, comprising:

(a) receiving a first set of data comprising an intensity value for each of a plurality of features associated with a probe array, and a crosstalk parameter for the first set of data; and

(c) applying the crosstalk parameter to each intensity value in the first set of data to produce a second set of data.

27. The method of claim 26, wherein:

the crosstalk parameter represents a measure of feature leakage.

28. The method of claim 27, wherein:

feature leakage includes an intensity contribution from a first feature to one or more neighboring features.

29. The method of claim 27, wherein:

feature leakage is the result of blurring.

30. The method of claim 29, wherein:

the blurring is associated with a point spread function of an optical instrument.

31. The method of claim 29, wherein:

a source of the blurring includes one or more of the group consisting of diffraction, spherical aberration, coma, defocus, vibration, turbulence in the air or liquid between the imaged object and the lens element, and temperature differences.

32. The method of claim 26, further comprising:

generating an image using the second set of data.

33. The method of claim 32, wherein:

the image is substantially the same as a true image of the probe array.