Analysis of data obtained from microarrays

Abstract

Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log 2 ratio data.

1 .- 10 . (canceled) 
     
     
         11 . A computer-implemented method of correcting a data set comprising one or more intensity values from a microarray experiment, the method comprising:
 scanning, by a scanning device, one or more nucleic acid samples hybridized to a nucleic acid probe mounted on a microarray used for the microarray experiment such that a data set comprising one or more intensity values from the microarray experiment is obtained;   detecting, by a processor, one or more artifacts in the data set by calculating logarithmic ratio values of at least some of the one or more intensity values based on one or more reference values stored in a memory, and using the logarithmic ratio values to detect signal gradients in the data set;   applying, by the processor, at least a filter to the logarithmic ratio values to remove the one or more artifacts, thereby generating a filtered data set;   applying, by the processor, one or more algorithms to the filtered data set to normalize the filtered data set at least with respect to one of intensity or color, thereby generating a corrected data set; and   displaying at least a portion of the corrected data set as a graphical presentation within an electronic user interface.   
     
     
         12 . The method of  claim 11 , wherein the one or more artifacts are caused by a variation in shading on a surface of the microarray. 
     
     
         13 . The method of  claim 12 , wherein the variation in shading on the surface of the microarray is an artificially highlighted color in at least one region of the surface of the microarray. 
     
     
         14 . The method of  claim 12 , wherein the variation in shading on the surface of the microarray is an artificially depressed color in at least one region of the surface of the microarray. 
     
     
         15 . The method of  claim 11 , wherein at least one of the one or more reference values corresponds to a theoretical plane having no signal intensity or color variation. 
     
     
         16 . The method of  claim 15 , wherein the theoretical plane is a two-dimensional plane. 
     
     
         17 . The method of  claim 11 , wherein the logarithmic ratio values are log 2 ratios. 
     
     
         18 . The method of  claim 11 , wherein the logarithmic ratio values are centered at a value of zero. 
     
     
         19 . The method of  claim 11 , wherein the one or more algorithms are applied to the filtered data set to remove a spatial bias. 
     
     
         20 . The method of  claim 11 , wherein the one or more algorithms are applied to the filtered data set to lower a level of background noise in the filtered data set. 
     
     
         21 . The method according to  claim 11 , wherein the one or more algorithms comprise Bayes wavelet shrinkage to reduce variations in the logarithmic ratio values. 
     
     
         22 . The method according to  claim 21 , further comprising:
 transforming, by the processor, the logarithmic ratio values using a Haar wavelet basis.   
     
     
         23 . The method of  claim 11 , wherein the microarray comprises a solid substrate. 
     
     
         24 . The method according to  claim 11 , wherein the microarray experiment comprises an expression level determination experiment. 
     
     
         25 . The method according to  claim 11 , wherein the microarray experiment comprises a copy number determination experiment. 
     
     
         26 . The method of  claim 11 , further comprising determining a copy number based on the corrected data set. 
     
     
         27 . The method according to  claim 11 , wherein the data set comprises one or more intensity values obtained from a microarray experiment conducted on a human DNA sample. 
     
     
         28 . The method according to  claim 11 , wherein the one or more nucleic acid samples comprise a labeled human DNA sample and the one or more intensity values are obtained by scanning fluorescence intensities of the labeled human DNA sample hybridized to nucleic acid probes on the microarray. 
     
     
         29 . The method according to  claim 11 , wherein the graphical presentation indicates at least one of expression levels, genotypes, copy numbers, and loss of heterozygosity (LOH) for the microarray experiment based on the corrected data set.