US6862363B2
Expired / Lapsed
US
⏱️ 0.0 years remaining
Image metrics in the statistical analysis of DNA microarray data
Assignee: Applied Precision Holdings LLC
•
Filing: 2001-01-25
•
Granted: 2005-03-01
•
Expires: 2021-01-25
Abstract
Abstract Expression profiling using DNA microarrays is an important new method for analyzing cellular physiology. In “spotted” microarrays, fluorescently labeled cDNA from experimental and control cells is hybridized to arrayed target DNA and the arrays imaged at two or more wavelengths. Statistical analysis is performed on microarray images and show that non-additive background, high intensity fluctuations across spots, and fabrication artifacts interfere with the accurate determination of intensity information. The probability density distributions generated by pixel-by-pixel analysis of images can be used to measure the precision with which spot intensities are determined. Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database. Error estimates from image-based metrics should be one component in an explicitly probabilistic scheme for the analysis of DNA microarray data.
Inventors
- 👤 Carl S. BROWN
- 👤 Paul C. GOODWIN
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-09 12:20
CPC Classifications
G; G06; G06T; G06T7/00; G06T7/0002; G06T7/0012; G06T7/40; G06T7/41; G06T2207/00; G06T2207/30; G06T2207/30004; G06T2207/30072
Claims Analysis
Total Claims: 23
Claim 1
Independent Claim
100 words
A method of determining a background intensity of an image; the method comprising: selecting a plurality of spots within the image falling within a least squares curve fit; and responsive to the selecting, determining a constant background intensity for the spots within the curve fit; wherein the least squares curve fit is determined from the equation: r m =R ( g m −g b )+ r b =Rg m +k where r m and g m are the measured values of the images, r b and g b are the background intensities of the images, and k is a constant.
Claim 2
Independent Claim
100 words
A method of determining a background intensity of an image; the method comprising: selecting a plurality of spots within the image falling within a least squares curve fit; and responsive to the selecting, determining a constant background intensity for the spots within the curve fit; wherein the least squares curve fit is determined from the equation: r m =R ( g m −g b )+ r b =Rg m +k where r m and g m are the measured values of the images, r b and g b are the background intensities of the images, and k is a constant.
Claim 3
Dependent Claim
21 words
The method of claim 1 , further comprising applying a constraint so the background intensities are greater than the bias levels.
Claim 4
Dependent Claim
54 words
The method of claim 1 , further comprising applying a constraint so the background intensities create a zero intercept of a linear regression of the equation: ( r m −r b )= m ( g m −g b )+ b such that b is approximately zero, which occurs when b=mg b −r b .
Claim 5
Dependent Claim
13 words
The method of claim 3 , further comprising extracting the background subtraction constants.
Claim 6
Independent Claim
42 words
A method of qualifying an individual microarray spot intensity ratio comprising: determining a ratio coefficient of variation of the spot; comparing the ratio coefficient of variation to a predetermined threshold; and qualifying the individual microarray spot intensity ratio responsive to the comparing.
Claim 7
Independent Claim
42 words
A method of qualifying an individual microarray spot intensity ratio comprising: determining a ratio coefficient of variation of the spot; comparing the ratio coefficient of variation to a predetermined threshold; and qualifying the individual microarray spot intensity ratio responsive to the comparing.
Claim 8
Dependent Claim
57 words
The method of claim 5 , further comprising determining the ratio coefficient of variation from the equation: CV = R SD R where R SD ≈ g SD 2 r _ 2 g _ 4 + r SD 2 g _ 2 - 2 σ rg r _ g _ 3 .
Claim 9
Dependent Claim
15 words
The method of claim 5 , further comprising determining a spot ratio coefficient of variation.
Claim 10
Dependent Claim
21 words
The method of claim 5 , further comprising determining an average ratio coefficient of variation of the spots within a microarray.
Claim 11
Independent Claim
47 words
A method of extracting data from an image comprising: determining a covariance and a variance of a microarray spot; normalizing the covariance; determining a mean and a standard deviation of the covariance; and selecting the data based on the mean and the standard deviation of the covariance.
Claim 12
Independent Claim
47 words
A method of extracting data from an image comprising: determining a covariance and a variance of a microarray spot; normalizing the covariance; determining a mean and a standard deviation of the covariance; and selecting the data based on the mean and the standard deviation of the covariance.
Claim 13
Dependent Claim
44 words
The method of claim 9 , further comprising calculating the covariance according to the following equation: σ rg = 1 n ∑ i = 1 n ( r i - r _ ) ( g i - g _ ) .
Claim 14
Dependent Claim
58 words
The method of claim 9 , further comprising normalizing the covariance by adding the variances in quadrature according to the following equation: σ rg ′ = σ rg σ r 2 + σ g 2 , where σ′ rg is the normalized covariance, and σ′ r and σ′ g are the variances of the control and experimental channels.
Claim 15
Dependent Claim
60 words
The method of claim 9 , further comprising normalizing the covariance by adding the variances according to the following equation: σ rg ′ = σ rg [ ( σ r + σ g ) 2 ] , where σ′ rg is the normalized covariance, and σ r , and σ g are the variances of the control and experimental channels.
Claim 16
Dependent Claim
54 words
The method of claim 9 , further comprising normalizing the covariance by using a control channel variance according to the following equation: σ rg ′ = σ rg σ g , where σ′ rg is the normalized covariance, and σ r , and σ g are the variances of the control and experimental channels.
Claim 17
Dependent Claim
54 words
The method of claim 9 , further comprising normalizing the covariance by using an experimental channel variance according to the following equation σ rg ′ = σ rg σ r , where σ′ rg is the normalized covariance, and σ r , and σ g are the variances of the control and experimental channels.
Claim 18
Independent Claim
63 words
A method of qualifying microarrays comprising: determining a covariance and a variance of each microarray spot; determining a slope of a linear regression between the covariance and the variance of all the spots within the microarray; selecting outlying spots from a plot of the covariance versus the variance; and selecting microarrays based on the slope and a regression coefficient of the linear regression.
Claim 19
Independent Claim
63 words
A method of qualifying microarrays comprising: determining a covariance and a variance of each microarray spot; determining a slope of a linear regression between the covariance and the variance of all the spots within the microarray; selecting outlying spots from a plot of the covariance versus the variance; and selecting microarrays based on the slope and a regression coefficient of the linear regression.
Claim 20
Dependent Claim
16 words
The method of claim 15 , further comprising plotting each covariance value versus each variance value.
Claim 21
Dependent Claim
22 words
The method of claim 15 , further comprising ignoring data points not along the slope of the covariance plotted against the variance.
Claim 22
Dependent Claim
25 words
The method of claim 15 , further comprising performing linear regression of the covariance plotted against the variance to create a distribution of data points.
Claim 23
Dependent Claim
18 words
The method of claim 18 , further comprising selecting an image having a tight distribution of data points.
References Cited (Backward Citations)
US5208870A
Cited
US6319682B1
Cited
US6411741B1
Cited
US6245517B1
Cited
US6251601B1
Cited
US20020028021A1
Cited
US6404925B1
Cited
US6285449B1
Cited
US6564082B2
Cited
US20030068082A1
Cited
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 2008-02-29 | 2008-08-30 | 2009-03-01 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2012-02-29 | 2012-08-30 | 2013-03-01 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2016-02-29 | 2016-08-30 | 2017-03-01 | $7700.00 | Window Closed / Lapsed |