Abstract: A method and system for predicting a signal fluctuation due to a flow of gaseous fluid approximately transverse to an optical path between a stage and an interferometric measuring apparatus for determining a position of the stage in a direction of a stage movement. The method includes acquiring three interferometric signals of three parallel optical beams, lying within the flow of the gaseous fluid, reflected from predetermined portions of the stage, extracting a mutual signal fluctuation caused by fluctuations of the gaseous fluid properties from the three interferometric signals, and predicting a future fluctuation of the interferometric signals using a linear adaptive filter acting on the extracted mutual signal fluctuation. Prior to the processing with the adaptive filter, a low-pass filter removes high frequency stage motions, and an adaptive moving average algorithm removes low frequency stage motions.

Abstract: Methods, systems and recordable media for accurately reading and identifying high quality signals from a microarray feature. Signals may be identified and used regardless of their geographic/geometric locations and patterns within the feature zone. High quality signals may be read, identified and outputted from a microarray feature in a geometrically independent manner, such that the best quality signals are identified and useable, regardless of the locations or patterns in the region from which the best quality signals are outputted.

Abstract: Systems methods and recordable media for predicting multi-variable outcomes based on multi-variable inputs. Additionally, the models described can be used to predict the multi-variable inputs themselves, based on the multi-variable inputs, providing a smoothing function, acting as a noise filter. Both multi-variable inputs and multi-variable outputs may be simultaneously predicted, based upon the multi-variable inputs. The models find a critical subset of data points, or “tent poles” to optimally model all outcome variables simultaneously to leverage communalities among outcomes.

Abstract: Methods, systems and computer readable media for checking label integrity of labeled biopolymers in a sample assayed by chemical array analysis. A sample is divided into equal aliquots. At least first and second labels are incorporated into biopolymers contained in first and second aliquots of the equal aliquots, respectively. The labels are added to the aliquots in amounts expected to incorporate into the biopolymers of the respective aliquots to produce signals of proportional quantity when read from probes on a chemical array designed to couple with biopolymers of the aliquots. The aliquots are then combined into a single, multi-labeled sample having at least first-labeled biopolymers and second-labeled biopolymers. The multi-labeled sample is hybridized with probes on a chemical array. Signal values are read from the probes on the chemical array bound to labeled biopolymers from the multi-labeled sample.

Abstract: Methods, systems and computer readable media for checking label integrity of labeled biopolymers in a single sample assayed by chemical array analysis. At least first and second labels are incorporated into biopolymers in the single sample to produce a multi-labeled, single sample. The multi-labeled, single sample is hybridized with probes on a chemical array, and signal values are read from probes on the chemical array bound to a set of biopolymer sequences labeled with the at least first and second labels. First-labeled signal values from a probe, having the first label incorporated therein, are compared with second-labeled signal values from the probe bound to biopolymer having the second label incorporated therein.

Abstract: Methods, systems and computer readable media for fast linear regression for modeling effects of multiple variables on uni-variable or multi-variable outputs. The techniques are particularly advantageous for large data matrices representing nominal and/or ordinal variables in conjunction with one or more scalar variables. Because nominal variables tend to produce very large, yet very sparse matrices, techniques for condensing such matrices and implementing such condensed matrices in performance of linear regression calculations are also provided.

Abstract: Methods, systems and computer readable media for removing labeling-bias factors affecting data from two or more data sources after single source biasing factors have been removed to the extent possible. Respective data points from the data sources are considered in combination to generate a population of data points. The population of data points is subdivided into portions of the overall population and, for each portion, the data points are sorted within that portion, relative to values of all other data values in that portion. A function is then generated for each portion from the sorted data points for that portion. For each portion, a value representative of highest population density of data points within that portion is identified. The identified values are fitted to a predetermined curve, and values of all data points are adjusted relative to the fitted values.

Abstract: Methods, systems and computer readable media for calibrating a device for which it is not possible to provide another device having a higher degree of precision to be used as a standard against which the device to be calibrated can be compared to perform the calibration. Metrology for interpreting the input and output fields and monitoring and supervising tasks of the device, and having sufficient accuracy, may be used to facilitate calibration.

Abstract: Methods, systems and computer readable media for imposing monotonic consistency among results of multiple platforms measuring the same specific property for the same/equivalent series of samples, to provide viable comparisons of sensitivity and precision among the platforms as well as provide useful conversion formulas among the platforms to ensure equivalent quantitation.

Abstract: Methods, systems and computer readable media for discovering a combination of treatments to reduce the progress of, or eliminate a tissue malady. Gene expression values of at least one sample of tissue exhibiting the tissue malady and at least one reference sample tissue that does not exhibit the malady are measured using at least one CGH array designed to measure gene sequences and possible variations in gene sequences attributable to the malady. Gene expression signatures are generated from differential expression values of ratios of the measured gene expression values between the at least one sample exhibiting the malady and the at least one reference sample, across all samples, respectively. The tissue samples exhibiting the malady are treated with a treatment, and a treatment-response value is measured with respect to each of the tissue samples treated, as effected by the treatment.

Abstract: Methods, systems and computer readable media for producing a metric to characterize a chemical array. Effects of terms impacting results of measurement of an output generated from analysis of the array or a procedure performed using the array, are quantified by performing ANOVA analysis and calculating sums of squares quantities attributable to each of the terms respectively. A metric is derived from at least two of the calculated sum of squares quantities. Methods systems and computer readable media for characterizing one or more chemical arrays may perform the steps of querying a database storing sums of squares quantities quantifying effects of terms impacting results of measurements of outputs generated from a plurality of chemical arrays; selecting sums of squares quantities based on the querying; and generating a metric based on the at least two sums of squares quantities.

Abstract: Methods, systems and computer readable media for differential clustering of gene expression response profiles for identification of potential functionally variant genes in a high throughput manner. Gene expression data is provided for a number of samples. Gene expression response profiles are generated for various sets of the samples and then differentially clustered across such sets to observe genes whose expression response profiles change cluster membership going from one set to another. Statistical analysis is performed with regard to the change from one cluster membership to another to determine whether the change from one cluster membership to another is statistically significant. If the change is determined to be statistically significant, the gene represented by the gene expression response profiles having been analyzed is identified as being a potential functionally variant gene. The nature of the function change may also be identified by the present systems, methods and computer readable media.

Abstract: Using contextual response profiles to group genes into “equivalent” classes to infer biological functionality. Comparing such classes from different contexts (conditions) to identify genes that change functionality. Also, methods, systems and computer readable media to separate gene expression signatures and distinguish differential gene expression specific to pure tissue in a heterogeneous tissue sample. Further, methods, systems and computer readable media for validating or calibrating a plotted curve of sorted p-values is provided. Still further, methods, systems and computer readable media are provided for distinguishing differentially expressed genes based on plotting expression levels and replicates derived from one or more genes in a first sample against corresponding expression levels and replicated derived from one or more genes in a second sample.

Abstract: Methods, systems and computer readable media for imposing monotonic consistency among results of multiple platforms measuring the same specific property for the same/equivalent series of samples, to provide viable comparisons of sensitivity and precision among the platforms as well as provide useful conversion formulas among the platforms to ensure equivalent quantitation.

Abstract: Data from a biological assay are analyzed and corrected to deconvolve and estimate the expression of a target material using the measured signals from a target probe and on or more homologous probes. The expressions of target and non-target material in a biological sample are allocated to the measured signals of multiple probes. The SIAM is used to correct the biological assay data to obtain more accurate results for the true expression.

Abstract: Methods, systems and recordable media for accurately reading and identifying high quality signals from a microarray feature. Signals may be identified and used regardless of their geographic/geometric locations and patterns within the feature zone. High quality signals may be read, identified and outputted from a microarray feature in a geometrically independent manner, such that the best quality signals are identified and useable, regardless of the locations or patterns in the region from which the best quality signals are outputted.

Abstract: Methods, systems and recordable media for using expression data characterizing protein pathways of diseases to produce phase relationships between treatment responses of diseased tissues to treatments applied thereto and expression profiles of the diseased tissues as measured when untreated. Methods, systems and recordable media for augmenting an original or existing treatment or treatment combination with one or more treatments that cover gene activity of a disease not addressed by the original/existing treatment.

Abstract: The present invention relates to a thermoplastic, multi-layer, electrostatic discharging, laminate comprised of at least one outer layer that is permanent static dissipative and non-contaminating, and a core or base layer that is conductive. The outer layer has a surface resistivity of from about 1.0×105 to about 1.0×1012 Ohm/sq, and the core layer has a surface resistivity of from about 1.0×101 to about 1.0×1011 Ohm/sq.

Abstract: The present invention relates to a thermoplastic, multi-layer, electrostatic discharging, laminate comprised of at least one outer layer that is permanent static dissipative and non-contaminating, and a core or base layer that is conductive. The outer layer has a surface resistivity of from about 1.0×105 to about 1.0×1012 Ohm/sq, and the core layer has a surface resistivity of from about 1.0×101 to about 1.0×1011 Ohm/sq.

Abstract: A method and apparatus for controlling trajectory in a scan and step wafer stepper are described. A control computer controls the motion of a stage by accelerating the stage during an acceleration period. The computer commands the stage to move at a constant velocity during a working period that starts after an end of the acceleration period, so that acceleration of the stage is continuous at the endpoints of the acceleration period. The stage is accelerated and moved so that jerk of the stage is zero and continuous at the endpoints of the acceleration period. The stage may be adapted to support a workpiece. The workpiece may be a semiconductor wafer, in which case the computer causes the wafer to be exposed to radiation during the working period.