Method and system for quantifying and removing spatial-intensity trends in microarray data

A program on physical computer readable media configured to, when executed, provide a computer user interface comprising:

• a listing of each microarray data set stored in a microarray database;
• an optional debug mode;
• a scrollable display listing available filters;
• a selection window for selecting optional moving-window filtering;
• an input window for inputting a size of the optional moving-window filter;
• an input window for selecting a fraction of selected filtered features;
• an input window for selecting an increment of the moving window filter;
• and
• a display window for displaying metric values for each microarray data set that allows a user to determine which surfaces are added to the database.

A system for determining spatial intensity trends in microarrays data, the system comprising:

• a computer processor;
• a communications medium by which one or more microarray data sets are received by the microarray-data processing system;
• a program, stored in the one or more memory components and executed by the computer processor to perform a method that selects a set of features, based on intensity levels, from each channel of the microarray data set;
• determines surface intensities for each feature in the channel of the microarray data set based on the selected set of features;
• quantifies the spatial-intensity trends in each channel of the microarray data set based on the surface intensities;
• corrects feature intensities for each channel of the multi-channel, microarray data set based on the determined surface intensities;
• and performs at least one of:
• outputting a result of the method to a display;
• outputting a result of the method to memory;
• outputting a result of the method to a computer on a network;
• or outputting a result to a human user in human-readable format.