Apparatus, method, and computer program product for determining confidence measures and combined confidence measures for assessing the quality of microarrays
First Claim
1. An apparatus for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the system comprising:
- a memory for storing digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
a processor coupled with the memory for accessing the digital data therefrom, and for determining a confidence measure for each of at least a portion of the signals for which digital data is stored in the memory;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, wherein each data point is contained in an image snip having borders, and wherein the confidence measure is an open perimeter confidence measure for the data point, determined based on the percentage of the perimeter of a data point occupied by the border of its respective snip.
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Accused Products
Abstract
An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarry experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.
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Citations
45 Claims
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1. An apparatus for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the system comprising:
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a memory for storing digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
a processor coupled with the memory for accessing the digital data therefrom, and for determining a confidence measure for each of at least a portion of the signals for which digital data is stored in the memory;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, wherein each data point is contained in an image snip having borders, and wherein the confidence measure is an open perimeter confidence measure for the data point, determined based on the percentage of the perimeter of a data point occupied by the border of its respective snip. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A method for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the method comprising:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, wherein each data point is contained in an image snip having borders, and wherein the confidence measure is an open perimeter confidence measure for the data point, determined based on the percentage of the perimeter of a data point occupied by the border of its respective snip. - View Dependent Claims (15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26)
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20. A method for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples as set forth in claim 20, wherein the subset confidence measures include at least one confidence measure selected from a group consisting of a position offset confidence measure, a background contamination confidence measure, a signal contamination confidence measure, a ignored pixel percentage confidence measure, a open perimeter confidence measure, and a shape regularity confidence measure, and wherein the normalization of each of the confidence measure includes a weighting factor to determine the relative contribution of each confidence measure to the combined confidence measure.
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27. A computer program product for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the computer program product usable with a computer system including a processor, a memory coupled with the processor, an input coupled with the processor for receiving the set of signals, the computer program product comprising means, stored on a computer readable medium, for:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, wherein each data point is contained in an image snip having borders, and wherein the confidence measure is an open perimeter confidence measure for the data point, determined based on the percentage of the perimeter of a data point occupied by the border of its respective snip. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39)
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40. An apparatus for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the system comprising:
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a memory for storing digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
a processor coupled with the memory for accessing the digital data therefrom, and for determining a confidence measure for each of at least a portion of the signals for which digital data is stored in the memory;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples;
wherein each data point has an expected shape and an actual shape, and where a shape regularity confidence measure for the data point is determined based on a comparison of the actual shape with the expected shape.
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41. A method for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the method comprising:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has an expected shape and an actual shape, and where a shape regularity confidence measure for the data point is determined based on a comparison of the actual shape with the expected shape.
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42. A computer program product for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the computer program product usable with a computer system including a processor, a memory coupled with the processor, an input coupled with the processor for receiving the set of signals, the computer program product comprising means, stored on a computer readable medium, for:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has an expected shape and an actual shape, and where a shape regularity confidence measure for the data point is determined based on a comparison of the actual shape with the expected shape.
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43. An apparatus for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the system comprising:
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a memory for storing digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
a processor coupled with the memory for accessing the digital data therefrom, and for determining a confidence measure for each of at least a portion of the signals for which digital data is stored in the memory;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples;
wherein each data point has a perimeter, and where an open perimeter confidence measure for the data point is determined based on a percentage of the perimeter that is open.
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44. A method for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the method comprising:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, and where an open perimeter confidence measure for the data point is determined based on a percentage of the perimeter that is open.
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45. A computer program product for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the computer program product usable with a computer system including a processor, a memory coupled with the processor, an input coupled with the processor for receiving the set of signals, the computer program product comprising means, stored on a computer readable medium, for:
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receiving digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals;
determining a confidence measure for each of at least a portion of the signals;
the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and
wherein each data point has a perimeter, and where an open perimeter confidence measure for the data point is determined based on a percentage of the perimeter that is open.
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Specification