Extended dynamic range reading of chemical arrays

Abstract

Methods of reading chemical arrays are provided. Aspects of the methods include reading an array at a first and second detector gain setting to produce linked data sets of an array, where each reading may be made using a different detector gain setting. Aspects of the methods further include extracting features from the linked data sets, where in certain embodiments a merged data set feature extraction protocol is employed. Aspects of the invention further include programming for operating devices, e.g., chemical array readers, as well as readers comprising such programming.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a substrate carrying an array, such as may be fabricated by methods of the present invention;

FIG. 2 is an enlarged view of a portion of FIG. 1 showing multiple spots or features;

FIG. 3 is an enlarged illustration of a portion of the substrate in FIG. 2;

FIG. 4 provides a flow chart of an array reading process according to an embodiment of the invention;

FIG. 5 provides a flow chart of a feature extraction process according to an embodiment of the invention;

FIG. 6 provides a flow chart of an XDR array reading and feature extraction protocol according to an embodiment of the invention;

FIG. 7 schematically illustrates an embodiment of an optical reader system of the present invention;

FIG. 8 provides a graphical representation of the ratio of signal from high gain to low gain scan according to an embodiment of the invention.

Claims

1. A method of reading a chemical array, said method comprising: (a) positioning said array in a reading position of a chemical array reader;(b) reading said array a first time in said scan position at a first detector gain setting to produce a first data set; and(c) before moving said array out of said reading position re-reading said array at a second detector gain setting to produce a second data set.

2. The method according to claim 1, wherein said re-reading occurs immediately after said reading of said array a first time.

3. The method according to claim 2, wherein said method further comprises selecting whether to read said array in an extended dynamic range mode.

4. The method according to claim 3, wherein when a choice is made to read said array in an extended dynamic range mode, said second detector gain setting is less than said first detector gain setting.

5. The method according to claim 4, wherein said method further comprises selecting said first and second detector gain settings.

6. The method according to claim 1, wherein said method further comprises linking said first and second data sets.

7. The method according to claim 6, wherein said first and second data sets are linked by an identifier.

8. The method according to claim 7, wherein said identifier is a name identifier.

9. The method according to claim 1, wherein said method further comprises feature extraction from said first and second scan data sets.

10. The method according to claim 9, wherein said feature extraction comprises merging said first and second data sets into a merged data set.

11. A method of extracting features from two or more linked data sets of a chemical array, said method comprising: (a) determining whether said linked data sets should be merged or used separately; and(b) if a decision is made to merge said linked data sets; (i) converting signals in said linked data sets to background subtracted signals;(ii) combining said background-subtracted signals into a merged set.

12. The method according to claim 11, wherein prior to said combining step (ii) said method further comprises correcting background subtracted signals to account for differences in detector gain.

13. The method according to claim 12, wherein said correcting comprises adjusting said background subtracted signals from a second of said linked data sets by a detector gain difference correction factor.

14. The method according to claim 13, wherein said detector gain difference correction factor is determined by: (a) defining an acceptable signal range;(b) determining the median of the ratios of the signals from said linked data sets that fall within said acceptable signal range to determine the detector gain difference correction factor.

15. The method according to claim 11, wherein said combining comprises selecting data from a given set based on whether a signal in a first set exceeds a threshold.

16. The method according to claim 11, wherein said combining comprises producing a merged set of signals in which signals from saturated features from a first of said linked data sets are substituted by signals from corresponding features from a second of said linked data sets.

17. The method according to claim 11, wherein said combining comprises averaging background subtracted signals from said linked data sets.

18. A computer-readable medium encoding instructions to direct a chemical array reader to perform the method of claim 1.

19. A chemical array reader comprising or communicating with a computer-readable medium according to claim 18.

20. A method of assaying a sample, said method comprising: (a) contacting said sample with a chemical array of two or more ligands immobilized on a surface of a solid support at different known locations; and(b) reading said array with a chemical array reader according to claim 19 to obtain two or more linked images of said array.

21. The method according to claim 20, wherein said method further comprises extracting features from said two or more linked images.

22. The method according to claim 21, wherein features are extracted from said two or more linked images using a feature extraction method according to claim 11.

23. The method according to claim 20, wherein said chemical array is chosen from a polypeptide array and a nucleic acid array.

24. A computer-readable medium encoding instructions to direct a computer to perform the method of claim 11.

25. A computer comprising a computer-readable medium according to claim 24.