Abstract: Methods for correcting systematic errors in the measured position of deposited features of a nucleic acid array on a substrate. Systematic errors are modeled by an algorithmic model based on measuring the positions (and possibly other properties) of a subset of the features, and a model is constructed for predicting deviations in feature position from an ideal grid. Deviations arising in the deposition process, the scanning process, or both may be corrected.

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 apparatus, and computer program products for generating and using an addressable array of chemical moieties on a substrate. In a processing unit may retrieve array related data from a memory. Such array related data may comprise any of data on a characteristic of the fabricated array, an instruction for reading an array, or an instruction on processing data from a read array. The processing unit may automatically access a program routine for reading the array or processing data from the read array based on the retrieved data.

Abstract: Methods of using an addressable array of biopolymers which has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established. A definition of the shapes of the established regions of each set is saved in a memory. Each region of each set is processed according to a corresponding routine for that set.

Abstract: A method of using an addressable array of biopolymers on a substrate includes receiving the addressable array and an associated machine readable identifier carried on an array substrate or array housing. The array is exposed to a sample and read, and the identifier machine read as an identifier signal. Biological function data for one or more of the biopolymers is retrieved from a memory based on the identifier signal. Other methods in which first and updated sets of feature characteristic data may readily be provided to array users, and methods of generating arrays are also provided, as are apparatus and computer program products which can execute a method for generating or using arrays.

Abstract: A method of generating an addressable array of biopolymers, such as DNA probes, on a substrate. The method includes receiving from a remote station, information on a layout of the array and an associated first identifier. A local identifier is generated corresponding to the first identifier and associated array, the local identifier being shorter in length than the corresponding first identifier. The addressable array is fabricated on the substrate in accordance with the received layout information. A first copy of the local identifier is applied to the substrate or a housing carrying the substrate. The fabricated array and the first copy of the local identifier are shipped to a remote user station. A method at the corresponding user station, and apparatus and computer program products useful at either station, are further provided.