Systems and methods for evaluating the significance of differences in biological measurements

• US 7,565,251 B2
• Filed: 12/12/2005
• Issued: 07/21/2009
• Est. Priority Date: 12/28/1998
• Status: Expired due to Fees

• Current Assignee: Microsoft Technology Licensing LLC (Microsoft Corporation)
• Original Assignee: Rosetta Inpharmatics LLC (Merck & Co., Inc.)
• Inventors: Stoughton, Roland, Dai, Hongyue
• Primary Examiner(s): Moran; Marjorie
• Assistant Examiner(s): Skowronek; Karlheinz R
• Application Number:
  US11/303,121
• Publication Number:
  US 20060190191A1
• Time in Patent Office: 1,317 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: Y10T 436/10 Composition for standardization, calibration, simulation, stabilization, preparation or preservation; processes of use in preparation for chemical testing

Abstract

A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

Claims

1. A method of estimating a significance d in a difference between a measurement of a cellular constituent in a first microarray experiment and a measurement of the cellular constituent in a second microarray experiment comprising:

computing on a suitably programmed computer

$d=\frac{\left(X-Y\right)}{\sqrt{{\mathrm{\sigma <br><br>}}_X^2+{\mathrm{\sigma <br><br>}}_Y^2+f^2<br><br>\left(X^2+Y^2\right)}}$

 

wherein

X is a brightness of a probe spot representing said cellular constituent in said first microarray experiment;

Y is a brightness of a probe spot representing said cellular constituent in said second microarray experiment;

σ

_X² is a variance term for X that represents an additive error level in X;

σ

_Y² is a variance term for Y that represents an additive error level in Y;

f is a fractional multiplicative error level;

σ

_X²+f²X² is an estimated variance for X; and

σ

_Y²+f²Y² is an estimated variance for Y.

2. The method of claim 1, wherein the first microarray experiment and the second microarray experiment are performed on the same microarray.

3. The method of claim 1, wherein the first microarray experiment and the second microarray experiment are each performed on a different microarray.

4. The method of claim 1, wherein said second microarray experiment is a nominal repeat of said first microarray experiment.

5. The method of claim 1, wherein said first microarray experiment represents a baseline state of a biological system and said second microarray experiment represents a perturbed state of said biological system.

6. The method of claim 5, wherein the perturbed state of said biological system is achieved by exposing said biological system, when representing said baseline state, to a pharmacological agent.

7. The method of claim 5, wherein the perturbed state of said biological system is achieved by exposing said first biological system, when representing said baseline state, to a drug candidate.

8. The method of claim 5, wherein the perturbed state of said biological system is achieved by introducing an exogenous gene into the biological system when the biological system represents said baseline state.

9. The method of claim 5, wherein said perturbed state of said biological system is achieved by deleting a gene from said biological system when the biological system represents said baseline state.

10. The method of claim 5, wherein said perturbed state of said biological system is achieved by changing a culture condition of said biological system when the biological system represents said baseline state.

11. The method of claim 5, wherein said perturbed state of said biological system is due to the onset of a disease in said biological system.

12. The method of claim 5, wherein the biological system is a cell line, a cell culture, a tissue sample, an organ, or a multicellular organism.

13. The method of claim 5, wherein the biological system is a mammal.

14. The method of claim 5, wherein the biological system is a Homo sapien.

15. The method of claim 5, wherein the biological system is a yeast that is substantially isogenic to Saccharomyces cerevisiae.

16. The method of claim 5, wherein the baseline state represents the wild-type state of the biological system.

17. The method of claim 5, wherein the baseline state represents a different perturbed state of the biological system.