Interface Method And System For Genetic Analysis Data

Abstract

Aspects of the present invention describe a method and apparatus for viewing and interfacing with gene expression on a computer device. A computer based device interfaces with gene the expression data by representing a plate having one or more wells and their contents with a matrix of elements addressable along at least two-dimensions. Each of the elements in the matrix are processed and then distinguished based upon their passing and failing one or more metrics for gene expression data. The interface displays those values associated with the distinguished elements in the matrix using colors, shapes and symbols. Depending on the results, some of the elements in the matrix may be flagged and then filtered from the data set. Remaining gene expression values not filtered from the matrix of elements are displayed and processed further.

1 . A computer implemented method of interfacing with genetic analysis data, comprising;
 representing a plate having one or more wells and their contents with a matrix of elements addressable along at least two-dimensions;   distinguishing one or more elements in the matrix based upon their passing and failing one or more metrics for genetic analysis data; and   filtering values associated with the distinguished one or more elements in the matrix from a study in response to the one or more metrics.   
     
     
         2 . The method of  claim 1  wherein the filtering improves analysis of the genetic analysis data. 
     
     
         3 . The method of  claim 1  wherein representing the plate includes displaying a graphical representation of the matrix on a display device. 
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . The method of  claim 1  wherein the distinguishing further comprises,
 associating an element in the matrix with a first geometric shape when the well has passed all metrics specified for the well; and 
 associating a second element in the matrix with a second geometric shape when the well has not passed all the metrics specified for the well. 
 
     
     
         7 . The method of  claim 1  further comprising:
 marking an element in the matrix with a first geometric shape and a first color to indicate that the well has passed both specified and unspecified metrics; and 
 marking an element in the matrix with the first geometric shape and a second color to indicate that the well passed the specified metrics and yet failed the unspecified metrics. 
 
     
     
         8 . The method of  claim 1  further comprising:
 marking an element in the matrix with a second geometric shape and third color when the well has not passed all the metrics specified for the well. 
 
     
     
         9 . The method of  claim 1  further comprising:
 marking an element in the matrix with a first geometric shape and third color around the border of the first geometric shape and a contrasting color to the third color as a fill color on the interior of the first geometric shape when the well has not passed all the metrics specified for the well. 
 
     
     
         10 . The method of  claim 1  further comprising:
 labeling each element in the matrix with a numeric value indicating a total number metrics associated with the element in the matrix and determined to have failed. 
 
     
     
         11 . The method of  claim 1  wherein an element in the matrix represents a portion of data from a set of datasets including: a value from a well in a plate, an aggregate of values from a plate in a study, an aggregate of values from a study in an experiment and an aggregate of values from an experiment in a clinical trial. 
     
     
         12 . The method of  claim 1  wherein the metrics are designed for performing quality control to improve reliability of the data represented by an element in the matrix. 
     
     
         13 . The method of  claim 1  wherein filtering values associated with the distinguished one or more elements, further comprises:
 specifying an application of one or more metrics to values associated with the one or more elements of the matrix; and 
 omitting the values associated with the one or more elements from further genetic analysis depending on the results from the application of the one or more metrics. 
 
     
     
         14 . The method of  claim 1  wherein filtering values associated with the distinguished one or more elements, further comprises:
 specifying an application of one or more metrics to values associated with the one or more elements of the matrix; and 
 including the values associated with the one or more elements in further genetic analysis depending on the results from the application of the one or more metrics. 
 
     
     
         15 . The method of  claim 13  wherein the results from the application of the one or more metrics are compared with a threshold value to decide if the values should be omitted. 
     
     
         16 . The method of  claim 12  wherein the metrics for quality control further comprise:
 receiving gene expression data associated with at least one spectral species and genetic sample in each well of a plate; 
 performing one or more gene expression related operations on data derived for each of the wells of the plate; 
 identifying gene expression data determined to have anomalous characteristics according to a set of one or more quality control metrics; and 
 flagging one or more wells of the plate affected by the anomalous characteristics according to quality control metrics. 
 
     
     
         17 . The method of  claim 16  further comprising:
 flagging one or more studies using the plate determined to have at least one or more wells flagged for the anomalous characteristics according to quality control metrics. 
 
     
     
         18 . The method of  claim 16  further comprising:
 determining whether to remove selected data associated with the flagged wells based upon the metrics for quality control; 
 excluding selected flagged data from gene expression related operations and indicate flagged wells. 
 
     
     
         19 . The method of  claim 16  further comprising:
 selecting a set of one or more quality control metrics for automating the quality control of the genetic analysis according to a type of assay and experiment being performed. 
 
     
     
         20 . (canceled) 
     
     
         21 . The method of  claim 20 , wherein the set of one or more metrics for quality control is selected from a set of quality control metrics including: a sensor saturation analysis, a bad passive reference analysis, missing data analysis, an empty well analysis, a large composite signal error analysis, a low laser power analysis, a non-amplified well analysis, a non-amplified plate analysis, a noise spike analysis, a high-relative noise analysis, a distance between clusters analysis, Ct failure analysis, a number of clusters analysis, exponential region failure analysis, a Hardy Weinberg analysis, a proportion of outliers analysis, a small sample number in cluster, baselining failure analysis, and thresholding analysis. 
     
     
         22 . (canceled) 
     
     
         23 . A computer program product for interfacing with gene expression data, tangibly stored on a computer-readable medium, comprising instructions operable to cause a programmable processor to:
 represent a plate having one or more wells and their contents with a matrix of elements addressable along at least two-dimensions;   distinguish one or more elements in the matrix based upon their passing and failing one or more metrics for gene expression data; and   filter values associated with the distinguished one or more elements in the matrix from a study in response to the one or more metrics.   
     
     
         24 . An apparatus for interfacing with gene expression data, comprising;
 means for representing a plate having one or more wells and their contents with a matrix of elements addressable along at least two-dimensions;   means for distinguishing one or more elements in the matrix based upon their passing and failing one or more metrics for gene expression data; and   means for filtering values associated with the distinguished one or more elements in the matrix from a study in response to the one or more metrics.