Claims
- 1. A method, comprising the steps of:
receiving first emission intensity data and second emission intensity data corresponding to probes of a probe array; determining first and second genotype calls for one or more probe sets, each having one or more probes, based, at least in part, on the first and second emission intensity data; comparing a first of the first genotype calls with a corresponding first of the second genotype calls and with a reference value; and displaying a measure of normalized change between the first and second genotype calls based, at least in part, on the comparison of first and second genotype calls and reference value.
- 2. The method of claim 1, wherein:
the emission intensity data includes a statistical measure of pixel values corresponding to the probes.
- 3. The method of claim 1, wherein:
the probe array includes a synthesized probe array or spotted probe array.
- 4. The method of claim 1, wherein:
the genotype call includes a biallelic call.
- 5. The method of claim 4, wherein:
the biallelic call includes combinations of two alleles.
- 6. The method of claim 4, wherein:
the biallelic call includes a relative allele signal that includes a numerical value between a range, wherein calls near one extreme of the range correspond to one type of homozygous call, calls near the opposing extreme of the range correspond to a second type of homozygous call, and intermediate calls in an intermediate sub-range within the range correspond to a heterozygous call.
- 7. The method of claim 1, wherein:
the reference value includes a standard deviation value.
- 8. The method of claim 1, wherein:
the step of displaying a measure of normalized change includes displaying a graphical user interface.
- 9. The method of claim 8, wherein:
the graphical user interface includes data displayed in a text format.
- 10. The method of claim 8, wherein:
the graphical user interface includes data displayed in a graphical format.
- 11. The method of claim 8, wherein:
the graphical user interface includes one or more associations of identification data with the measure of normalized change.
- 12. The method of claim 11, wherein:
the identification data includes any one or combination of a probe set identifier, one or more SNP locations, one or more genotype calls, or one or more relative allele signals.
- 13. The method of claim 12, wherein:
the one or more SNP locations include chromosome number or estimated genetic distance.
- 14. The method of claim 13, wherein:
the estimated genetic distance is a relative measure of a distance from a SNP location to the top of the short arm of a chromosome.
- 15. The method of claim 14, wherein:
the estimated genetic distance is expressed in centimorgans.
- 16. The method of claim 8, wherein:
the identification data is displayed in a geometric association with the measure of normalized change.
- 17. The method of claim 15, wherein:
the geometric association includes a column or row of graphical or textual elements.
- 18. The method of claim 8, wherein:
the identification data is displayed in a color, shade, or intensity association with the measure of normalized change.
- 19. A method, comprising the steps of:
receiving first emission intensity data and second emission intensity data corresponding to probes of a probe array, wherein the first and second emission intensity data include a statistical measure of pixel values corresponding to the probes; determining first and second genotype calls for one or more probe sets, each having one or more probes based, at least in part, on the first and second emission intensity data; comparing a first of the first genotype calls with a corresponding first of the second genotype calls; and displaying a measure of normalized change between the first and second genotype calls.
- 20. The method of claim 19, wherein:
the measure of normalized change is based, at least in part, on the comparison of first and second genotype calls and reference value.
- 21. A computer program product, comprising:
an input manager constructed and arranged to receive first emission intensity data and second emission intensity data corresponding to probes of a probe array; a genotype analysis determiner constructed and arranged to determine first and second genotype calls for one or more probe sets, each having one or more probes based, at least in part, on the first and second emission intensity data; a genotype comparator constructed and arranged to compare a first of the first genotype calls with a corresponding first of the second genotype calls and with a reference value; and an output manager constructed and arranged to display a measure of normalized change between the first and second genotype calls.
- 22. The computer program product of claim 21, wherein:
the measure of normalized change is based, at least in part, on the comparison of first and second genotype calls and reference value.
- 23. A method, comprising the steps of:
receiving one or more sets of emission intensity data corresponding to probes of a biological probe array; determining absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter; and displaying the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter.
- 24. The method of claim 23, wherein:
the probe array includes a synthesized or spotted probe array.
- 25. The method of claim 23, wherein:
the absolute expression value includes a detection call, wherein the detection call includes a present, absent, or no call.
- 26. The method of claim 23, wherein:
the relative expression value includes a change of expression call, wherein the change of expression call includes increase, decrease, or no change.
- 27. The method of claim 23, wherein:
the statistical measure includes a p-value that is within a range between a first extreme value and an opposing second extreme value.
- 28. The method of claim 27, wherein:
the p-value is a measure of absolute expression, wherein a p-value near the first extreme value indicates the presence of expression and a p-value near the second extreme value indicates the absence of expression.
- 29. The method of claim 27, wherein:
the p-value is a measure of relative expression, wherein a p-value near the first extreme value indicates the presence of increased expression and a p-value near the second extreme value indicates the decrease of expression.
- 30. The method of claim 23, wherein:
the at least one user-selectable statistical parameter includes a threshold for calculation of the statistical measure, wherein the threshold accounts for experimental variation.
- 31. The method of claim 23, wherein:
the at least one user-selectable display parameter includes one or more values for the evaluation of the absolute or expression values.
- 32. A computer program product, comprising:
an input manager constructed and arranged to receive one or more sets of emission intensity data corresponding to probes of a biological probe array; a statistical analysis determiner constructed and arranged to determine absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter; and an output manager constructed and arranged to display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter.
- 33. A computer program product, comprising:
an input manager constructed and arranged to receive one or more sets of emission intensity data corresponding to probes of a biological probe array; and a genotype and statistical analysis manager constructed and arranged to determine absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter, and further constructed and arranged, when the one or more sets of emission intensity data include first and second sets of emission intensity data, to determine first and second genotype calls for one or more probe sets, each having one or more probes based, at least in part, on the first and second sets of emission intensity data, and further constructed and arranged to display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and a measure of normalized change between the first and second genotype calls based, at least in part, on the comparison of first and second genotype calls and reference value.
- 34. A system, comprising:
a scanner constructed and arranged to provide emission intensity data corresponding to probes of a biological probe array; and a computer constructed and arranged to execute a computer program product comprising (a) an input manager constructed and arranged to receive one or more sets of the emission intensity data, and (b) a genotype and statistical analysis manager constructed and arranged to determine absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter, and further constructed and arranged, when the one or more sets of emission intensity data include first and second sets of emission intensity data, to determine first and second genotype calls for one or more probe sets, each having one or more probes based, at least in part, on the first and second sets of emission intensity data, and further constructed and arranged to display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and a measure of normalized change between the first and second genotype calls based, at least in part, on the comparison of first and second genotype calls and reference value.
RELATED APPLICATIONS
[0001] The present application claims priority to U.S. Provisional Patent Application No. 60/312,906, titled “METHODS AND SYSTEMS FOR EVALUATING ALLELIC IMBALANCE AND PERFORMING OTHER GENOMIC ANALYSIS FUNCTIONS” filed Aug. 16, 2001, which is hereby incorporated by reference herein in its entirety for all purposes.
Provisional Applications (1)
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Number |
Date |
Country |
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60312906 |
Aug 2001 |
US |