Systems and Methods for Analyzing Microarrays

Abstract

The present invention discloses methods and systems for analyzing microarray data. The method includes the general steps of providing microarray data, normalizing the data using a least trimmed squares regression, and then analyzing the normalized microarray data to obtain a desired result such as an expression profile. There is also disclosed a method of subdividing an array into subarrays before normalization. This approach provides a method for improving measurement accuracy and salvaging array data from arrays containing minor defects. Also disclosed is a Probe-Treatment-Reference (PTR) model for streamlining normalization and summarization of microarray data by allowing multiple references. Other aspects of the present invention include computer systems and computer readable media encoding methods of the present invention.

1 - 21 . (canceled) 
     
     
         22 . A method for detecting defective areas on a microarray, comprising:
 dividing the array into a plurality of subarrays;   applying a normalization procedure comprising a least trimmed squares method or a symmetric variant thereof, wherein said least trimmed squares regression method of the symmetric variant thereof normalizes the microarray data by estimating parameters for a linear model and fitting the data to the model; and   estimating the parameters of the linear models across the plurality of subarrays to detect subarrays that are defective.   
     
     
         23 . A method for salvaging data from a defective micro-array, comprising:
 applying the method of  claim 22  to identify areas of the microarray that are defective; and   saving data from non-defective areas of the microarray for later processing, thereby, salvaging data from a defective micro-array.   
     
     
         24 . A computer implemented system for normalizing microarray data, comprising:
 a data input for receiving microarray data and user input;   a processing unit and a memory configured to normalize the microarray data by performing a least trimmed squares method or a symmetric variant thereof on the data, wherein the least trimmed squares method or variant thereof determines parameters for a linear model that fit the data and normalized the data based on the model; and   outputting the resulting normalized microarray data for further analysis.   
     
     
         25 . The system of  claim 24 , wherein the processing unit and memory are configured to further perform the step of subdividing the microarray data into subarrays before performing the normalizing step within each subarray. 
     
     
         26 . (canceled) 
     
     
         27 . A computer readable medium having encoded thereon a method according to  claim 22 . 
     
     
         28 . A computer readable medium having encoded thereon a method according to  claim 23 .