Abstract: A method and system for employing signal-intensity data contained within areas of a scanned image of a chemical array corresponding to features and feature backgrounds in order to determine whether or not the features or feature backgrounds have non-uniform signal intensities and are thus outlier features and outlier feature backgrounds. A signal intensity variance model is provided to dynamically adjust to the signals read from the scanned image of the array. Calculated variance from measured values of the signal intensities and pixel distributions within a feature or feature background is compared to a maximum allowable variance calculated for the feature or feature background based on the dynamically adjusting signal intensity variance model. When the calculated variance (from the measured values) is less than or equal to the maximum allowable variance, the feature or feature background is considered to have acceptable signal-intensity uniformity.

Abstract: Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated.

Abstract: Systems, tools and methods are used to perform complex sandwich hybridization assays of biological material. The tools comprise biological solution probes having a first region for hybridizing to capture probes on a universal assay apparatus, and a second region for hybridizing to a sample target. The solution probe assembles the target to the apparatus by hybridizing the second region to the target and the first region to the capture probe. Multiple biological samples, having a plurality of targets per sample, can be multiplexed on the same universal array. The customized solution probe addresses and assembles a predetermined target-sample combination onto the array at a corresponding capture probe address location. Specificity and sensitivity of the assay are provided by the incorporation of a modified monomer in the capture probe and a similarly modified monomer complement in the first region of the solution probe. The modified monomers preferentially hybridize with each other.

Abstract: Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated.

Abstract: A method and system for employing signal-intensity data contained within areas of a scanned image of a chemical array corresponding to features and feature backgrounds in order to determine whether or not the features or feature backgrounds have non-uniform signal intensities and are thus outlier features and outlier feature backgrounds. A signal intensity variance model is provided to dynamically adjust to the signals read from the scanned image of the array. Calculated variance from measured values of the signal intensities and pixel distributions within a feature or feature background is compared to a maximum allowable variance calculated for the feature or feature background based on the dynamically adjusting signal intensity variance model. When the calculated variance (from the measured values) is less than or equal to the maximum allowable variance, the feature or feature background is considered to have acceptable signal-intensity uniformity.

Abstract: Systems, methods and computer readable media for characterizing a chemical array. At least one metric indicative of accuracy of location of features on the chemical array by a feature extraction process used to extract signals from features of the chemical array may be generated, as well as additional metrics adapted to identify errors caused by a particular process used in generating the signals on the array. A quality control report may be generated to contain at least one metric indicative of accuracy of location and said at least one additional metric. Customized quality control reports may be generated by providing for user selection of at least one metric adapted to identify errors caused by a particular process used in generating signals on a chemical array, from plurality of metrics, and including such selections in the quality control report generated.

Abstract: A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Abstract: A method of processing one or more detected signal images each acquired from a field of view of a chemical array reader. A location correction is determined based on different detected signals at different image regions which represent regions in the field of view having the same actual signal. Alternatively or additionally, a location correction is applied to a detected signal at an image region. The location correction reduces detected signal discrepancy between different regions in an acquired image which represent different regions in the field of view having the same actual signal. An array reading system and computer program products are also provided.

Abstract: A method, apparatus, and computer program product for reading fluorescence signals from an array of chemical moieties (such as different sequence peptides or polynucleotides, for example different DNA sequences). In the method the spatial sequence of scanned locations need not be the same as the temporal sequence. For example, a later illuminated line may be spatially closer to an earlier illuminated line than is a temporally intervening illuminated line.

Abstract: Methods for substantially improved detection and analysis in nucleic acid hybridization assays are described. The methods provide the reliable estimation of background signal which derives primarily from nonspecific hybridization. The invention is useful in chemical, biological, medical and diagnostic techniques, as well as for drug discovery.

Abstract: The invention provides an apparatus and method for determining a signal produced by a micro array device. The apparatus provides an unstructured probe and structured probe. The unstructured probe binds to a target and provides a first signal that can be compared to a second signal produced by a structured probe. A more accurate level of intensity of the first signal can be determined by comparing to the second signal produced by the structured probe. A method for determining a more accurate level of signal intensity produced from the unstructured probes bound to the target is also disclosed.

Abstract: Nucleic acid arrays that have background features, and methods for using the same, are provided. The subject nucleic acid arrays include both hybridization features and background features, where the background features provide a background signal in a hybridization assay that is made up of a feature substrate component, a nucleic acid probe component and a nucleic acid probe non-specific binding component. In practicing the subject methods, the arrays are contacted with a sample and signals are observed for both hybridization features and background features. The background feature signal is then subtracted from the hybridization feature signal to obtain a background corrected hybridization feature signal that is employed as the output of the assay, e.g., to determine the presence, either qualitatively or quantitatively, of the analyte target nucleic acid in the sample. Also provided are kits for use in practicing the subject methods.

Abstract: Systems, tools and methods of assaying biological material are used to perform complex sandwich hybridization assays. The tools used comprise biological solution probes that are customized for each assay. The solution probe comprises a first region for hybridizing to a probe, in a generic set of capture probes on a universal assay apparatus, and a second region for hybridizing to a target in a sample. The solution probe assembles the target to the assay apparatus by hybridizing the second region to the target and the first region to the capture probe. In array assays, one or more biological samples, having one or more targets per sample, can be multiplexed on the same universal array comprising the generic set of capture probes in an array pattern of features on the substrate. The customized solution probe addresses and assembles a predetermined target-sample combination onto the array at a corresponding capture probe address location.

Abstract: A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

Abstract: A method and system for employing pixel-based, signal-intensity data contained within areas of a scanned image of a molecular array corresponding to features and feature backgrounds in order to determine whether or not the features or feature backgrounds have non-uniform signal intensities and are thus outlier features and outlier feature backgrounds. A calculated, estimated variance for the signal intensities within a feature or feature background is compared to a maximum allowable variance calculated for the feature or feature background based on a signal intensity variance model. When the experimental variance is less than or equal to the maximum allowable variance, the feature or feature background is considered to have acceptable signal-intensity uniformity. Otherwise, the feature or feature background is flagged as an outlier feature or outlier feature background.

Abstract: A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Abstract: Methods are provided for identifying heterogeneous features, including heterogeneous background regions, in an image of an array, e.g., in an image of a biopolymeric array, such as a nucleic acid array. The subject methods employ an algorithm that employs a different dispersity measure depending on whether the signal features are weaker or stronger. Also provided are computer readable storage media that include an algorithm capable of performing the steps of the subject methods. The subject methods find use in the processing of images obtained from a variety of different types of arrays, including nucleic acid arrays.

Abstract: A method of processing one or more detected signal images each acquired from a field of view of a chemical array reader. A location correction is determined based on different detected signals at different image regions which represent regions in the field of view having the same actual signal. Alternatively or additionally, a location correction is applied to a detected signal at an image region. The location correction reduces detected signal discrepancy between different regions in an acquired image which represent different regions in the field of view having the same actual signal. An array reading system and computer program products are also provided.

Abstract: A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Abstract: A method, apparatus, and computer program product for reading fluorescence signals from an array of chemical moieties (such as different sequence peptides or polynucleotides, for example different DNA sequences). In the method the spatial sequence of scanned locations need not be the same as the temporal sequence. For example, a later illuminated line may be spatially closer to an earlier illuminated line than is a temporally intervening illuminated line.