Rearrangement of microarray scan images to form virtual arrays

• US 6,950,756 B2
• Filed: 02/05/2003
• Issued: 09/27/2005
• Est. Priority Date: 02/05/2003
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Kincaid, Robert
• Primary Examiner(s): Martinell, James
• Application Number:
  US10/359,454
• Publication Number:
  US 20040153251A1
• Time in Patent Office: 965 Days
• Field of Search: 702/19, 702/20, 435/6
• US Class Current: 702/19
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A system and methods for selecting single-features from a microarray scan image of genomic data and rearranging the selected single-features of the microarray into a virtual array having a format or arrangement that is more relevant or informative to the analyst or user than that of the original microarray scan image.

Claims

1. A method of creating at least one virtual microarray scan image using at least one real microarray scan image, the method comprising:

providing at least one microarray scan image having an array of feature images;

accessing said at least one microarray scan image;

selecting feature images from said at least one real array of feature images;

singulating said selected feature images from said at least one real microarray scan image; and

rearranging said singulated feature images into at least one virtual microarray.

2. The method of claim 1, further comprising storing said at least one virtual microarray.

3. The method of claim 1, further comprising said presenting a visual image of said at least one virtual microarray for a user to visualize.

4. The method of claim 1, further comprising extracting data from at least one of said features in said at least one virtual microarray.

5. The method of claim 4, further comprising publishing said extracted data from said at least one virtual microarray.

6. The method of claim 1, wherein said singulating comprises cropping said selected feature images from said at least one microarray scan image.

7. The method of claim 1, wherein said selecting feature images comprises selecting features from two or more real microarray images.

8. The method of claim 7, wherein said rearranging said singulated feature images comprises rearranging said singulated feature images into two or more virtual arrays.

9. The method of claim 1, wherein said selecting feature images comprises selecting feature images which have probes which are up-regulated.

10. The method of claim 1, wherein said selecting feature images comprises selecting feature images which have probes which are down-regulated.

11. The method of claim 9 or 10 wherein said rearranging said singulated feature images comprises rearranging said feature images according to probe intensity.

12. The method of claim 1 wherein said selecting feature images comprises selecting feature images relevant to a specific medical diagnosis.

13. The method of claim 1 wherein said selecting feature images comprises selecting feature images relevant to a specific scientific measurement.

14. A method of creating at least one virtual microarray scan image using at least one real microarray scan image, the method comprising:

providing at least one real microarray scan image having an array of feature images;

accessing said at least one real microarray scan image;

providing at least one synthetic feature; and

overlaying or adding said at least one synthetic feature image to the real microarray scan image to form at least one virtual microarray.

15. The method of claim 14, further comprising extracting data from said at least one virtual microarray.

16. The method of claim 15, wherein said extracting data is performed using data extraction software.

17. The method of claim 16, further comprising validating said data extraction software used to perform said extracting.

18. The method of claim 14, further comprising storing said at least one virtual microarray.

19. The method of claim 14, further comprising presenting a visual image of said at least one virtual microarray for a user to visualize.

20. A computer readable medium carrying one or more sequences of instructions from a user of a computer system for creating at least one virtual microarray scan image using at least one real microarray scan image, wherein the execution of the one or more sequences of instructions by one or more processors cause the one or more processors to perform the steps of:

providing at least one real microarray scan image having an array of feature images;

accessing said at least one real microarray scan image;

selecting feature images of said at least one real microarray scan image;

singulating said selected feature images from said at least one real microarray scan image; and

rearranging said singulated feature images into at least one virtual microarray.

21. The computer readable medium of claim 20, wherein the following further step is performed:

storing said at least one virtual microarray in memory.

22. The computer readable medium of claim 20, wherein the following further step is performed:

presenting a visual image of said at least one virtual microarray for a user to visualize.

23. The computer readable medium of claim 20 wherein the following further step is performed:

extracting data from said at least one virtual array.

24. The computer readable medium of claim 20, wherein the following further step is performed:

publishing said extracted data from said at least one virtual array.

25. A computer readable medium carrying one or more sequences of instructions from a user of a computer system for creating at least one virtual microarray scan image using at least one real microarray scan image, wherein the execution of the one or more sequences of instructions by one or more processors cause the one or more processors to perform the steps of:

providing at least one real microarray scan image having an array of feature images;

accessing said at least one real microarray scan image;

providing at least one synthetic feature; and

overlaying or adding said at least one synthetic feature to said real microarray scan image to form at least one virtual microarray.

26. The computer readable medium of claim 25, wherein the following further step is performed:

extracting data from said at least one virtual microarray.

27. The computer readable medium of claim 26, wherein the following further step is performed:

validating the data extraction software used to perform said step of extracting.

28. The computer readable medium of claim 25, wherein the following further step is performed:

storing said at least one virtual microarray in memory.

29. The computer readable medium of claim 25, wherein the following further step is performed:

presenting a visual image of said at least one virtual microarray for a user to visualize.