Normalization of gene expression data

Abstract

A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.

1 . A method for determining bias across two domains comprising gene expression data, the method comprising: 
 providing a first domain and a second domain;    obtaining information indicative of a bias within the first domain;    obtaining information indicative of a bias within the second domain; and    using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.    
     
     
         2 . The method according to  claim 1 , wherein the providing a first domain and a second domain further comprises providing at least one of the first domain and the second domain comprising information collected from a polynucleotide amplification instrument.  
     
     
         3 . The method according to  claim 2  wherein the polynucleotide amplification instrument is capable of running polymerase chain reactions.  
     
     
         4 . The method according to  claim 1  wherein the providing a first domain and a second domain further comprises providing at least one of the first domain and the second domain comprising information generated by gene expression analysis.  
     
     
         5 . The method according to  claim 4  wherein the providing at least one of the first domain and the second domain comprise data generated by gene expression analysis comprising generating gene expression data from an polynucleotide amplification instrument.  
     
     
         6 . The method according to  claim 4  wherein the providing at least one of the first domain and the second domain comprise data generated by gene expression analysis comprising generating gene expression data from an microarray.  
     
     
         7 . The method according to  claim 4  wherein the providing at least one of the first domain and the second domain comprise data generated by gene expression analysis comprising generating gene expression data from a hybridization chip.  
     
     
         8 . The method according to  claim 1  wherein the providing a first domain and a second domain further comprises providing information from a preamplified and amplified sample and providing information from an amplified sample.  
     
     
         9 . The method according to  claim 1  further comprising amplifying a polynucleotide sample.  
     
     
         10 . The method according to  claim 9  further comprising collecting information indicative of the amplifying a polynucleotide sample.  
     
     
         11 . The method according to  claim 10  further comprising organizing the information indicative of the amplifying a polynucleotide sample into the first domain.  
     
     
         12 . The method according to  claim 9  further comprising preamplifying a polynucleotide sample.  
     
     
         13 . The method according to  claim 12  further comprising collecting information indicative of the preamplifying a polynucleotide sample and amplifying a polynucleotide sample.  
     
     
         14 . The method according to  claim 13  further comprising organizing the information indicative of the preamplifying a polynucleotide sample and amplifying a polynucleotide sample into the first domain.  
     
     
         15 . The method according to  claim 14  wherein the obtaining information indicative of bias within the first domain comprises evaluating a bias between the amplifying a polynucleotide sample and the preamplifying a polynucleotide sample and amplifying a polynucleotide sample.  
     
     
         16 . The method according to  claim 15  wherein the obtaining information indicative of bias within the second domain comprises evaluating a bias between the amplifying a second polynucleotide sample and the preamplifying a polynucleotide second sample and amplifying a second polynucleotide sample.  
     
     
         17 . The method according to  claim 16  wherein the polynucleotide sample and the second polynucleotide sample are from different tissues.  
     
     
         18 . The method according to  claim 17  wherein the different tissues are from the same individual.  
     
     
         19 . The method according to  claim 1  wherein the obtaining information indicative of bias within the first domain further comprises performing a ΔΔC T  calculation.  
     
     
         20 . The method according to  claim 1  wherein the obtaining information indicative of bias within the second domain further comprises performing a ΔΔC T  calculation.  
     
     
         21 . The method according to  claim 1  wherein the using the information indicative of bias within the first domain and the information indicative of bias within the second domain to produce an indication of bias across the two domains further comprises performing a ΔΔΔC T  calculation.  
     
     
         22 . The method according to  claim 1  wherein the obtaining information indicative of bias within the first domain comprises information from a first amplification device and the obtaining information indicative of bias within the second domain comprises from information a second amplification device.  
     
     
         23 . The method according to  claim 1  further comprising converting information from a micro array device into a ΔΔC T  format.  
     
     
         24 . The method according to  claim 23  the obtaining information indicative of bias within the first domain comprises information from a first amplification device and the obtaining information indicative of bias within the second domain comprises from information from a microarray device.  
     
     
         25 . The method according to  claim 1  wherein the obtaining information indicative of bias within the first domain comprises information from a first tissue type and the obtaining information indicative of bias within the second domain comprises from information a second tissue type.  
     
     
         26 . The method according to  claim 1  wherein the obtaining information indicative of bias within the first domain comprises information from gene expression of a first individual and the obtaining information indicative of bias within the second domain comprises from information from gene expression of a second individual.  
     
     
         27 . The method according to  claim 26  wherein the first individual and the second individual are from the same species.  
     
     
         28 . The method according to  claim 26  wherein the first individual and the second individual are from different species.  
     
     
         29 . The method according to  claim 1  further comprising applying a correction to at least one of the first domains and the second domains.  
     
     
         30 . The method according to  claim 29  wherein the applying a correction to at least one of the first domains and the second domains corrects for a bias across the first domain and the second domain.  
     
     
         31 . The method according to  claim 1  wherein at least one of the first domain and the second domain comprises genomic information.  
     
     
         32 . A method for determining bias across two domains comprising gene expression data, the method comprising: 
 providing a first domain comprising preamplified gene expression data and non-preamplified gene expression data from a first sample input;    determining a bias between the preamplified gene expression data and the non-preamplified gene expression data of the first domain;    providing a second domain comprising preamplified gene expression data and non-preamplified gene expression data from a second sample input.    determining a bias between the preamplified gene expression data and the non-preamplified gene expression data of the second domain.    using the bias of the first domain and the bias of the second domain to produce an indication of bias across the first domain and the second domain.    
     
     
         33 . The method according to  claim 32  further comprising amplifying the first sample input.  
     
     
         34 . The method according to  claim 33  further comprising collecting data from the amplifying the first sample input.  
     
     
         35 . The method according to  claim 33  further comprising adding a first reference to the first sample input.  
     
     
         36 . The method according to  claim 34  further comprising using the first reference to normalize data from the amplifying the first sample input.  
     
     
         37 . The method according to  claim 34  further comprising using a ΔC T  calculation to normalize data from the amplifying the first sample input.  
     
     
         38 . The method according to  claim 32  further comprising preamplifying the first sample input.  
     
     
         39 . The method according to  claim 38  further comprising amplifying the first sample input.  
     
     
         40 . The method according to  claim 39  further comprising collecting data from the amplifying the first sample input.  
     
     
         41 . The method according to  claim 39  further comprising adding a first reference to the first sample input.  
     
     
         42 . The method according to  claim 41  further comprising using the first reference to normalize data from the preamplifying and amplifying the first sample input.  
     
     
         43 . The method according to  claim 41  further comprising using a ΔC T  calculation to normalize data from the preamplifying and amplifying the first sample input.  
     
     
         44 . The method according claims  37  and  43  further comprising using a ΔΔC T  calculation to determine bias.  
     
     
         45 . The method according to  claim 32  further comprising amplifying the second sample input.  
     
     
         46 . The method according to  claim 45  further comprising collecting data from the amplifying the second sample input.  
     
     
         47 . The method according to  claim 45  further comprising adding a second reference to the second sample input.  
     
     
         48 . The method according to  claim 46  further comprising using the second reference to normalize data from the amplifying the second sample input.  
     
     
         49 . The method according to  claim 46  further comprising using a ΔC T  calculation to normalize data from the amplifying the second sample input.  
     
     
         50 . The method according to  claim 32  further comprising preamplifying the second sample input.  
     
     
         51 . The method according to  claim 50  further comprising amplifying the second sample input.  
     
     
         52 . The method according to  claim 51  further comprising collecting data from the amplifying the second sample input.  
     
     
         53 . The method according to  claim 50  further comprising adding a second reference to the second sample input.  
     
     
         54 . The method according to  claim 53  further comprising using the second reference to normalize data from the preamplifying and amplifying the second sample input.  
     
     
         55 . The method according to  claim 53  further comprising using a ΔC T  calculation to normalize data from the preamplifying and amplifying the second sample input.  
     
     
         56 . The method according claims  49  and  55  further comprising using a ΔΔC T  calculation to determine bias.  
     
     
         57 . A method according to  claim 32  wherein the using the bias of the first domain and the bias of the second domain to produce an indication of bias across the first domain and the second domain further comprises performing a ΔΔΔC T  calculation.  
     
     
         58 . A system for determining bias across two domains, the system comprising: 
 a first domain stored on a media;    a second domain stored on a media;    a first algorithm for obtaining information indicative of a bias within the first domain;    a second algorithm for obtaining information indicative of a bias in the second domain;    a third algorithm for using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains; and    an output.    
     
     
         59 . The system according to  claim 58  further comprising at least one computer.  
     
     
         60 . The system according to  claim 58  further comprising at least one PCR device.  
     
     
         61 . The system according to  claim 58  further comprising at least one microarray device.  
     
     
         62 . The system according to  claim 58  further comprising high density sequence detection system.  
     
     
         63 . The system according to  claim 58  further comprising at least one sample.  
     
     
         64 . The system according to  claim 58  further comprising a graphical use interface.  
     
     
         65 . The system according to  claim 58  further comprising a network.  
     
     
         66 . The system according to  claim 65  wherein the first domain and the second domain are at different loci on the network.  
     
     
         67 . The system according to  claim 58  further comprising a hybridization chip device.  
     
     
         68 . The system according to  claim 58  wherein at least one of the first algorithm, the second algorithm, and the third algorithm is a comparative method.  
     
     
         69 . The system according to  claim 58  wherein at least one of the first algorithm and the second algorithm is a ΔΔC T  calculation.  
     
     
         70 . The system according to  claim 58  wherein the third algorithm is a ΔΔΔC T  calculation.  
     
     
         71 . The system of  claim 58  wherein at least one of the first domain and the second domain comprises polynucleotide information.  
     
     
         72 . The system of  claim 58  wherein at least one of the first domain and the second domain comprises gene expression information.  
     
     
         73 . The system of  claim 58  wherein at least one of the first domain and the second domain comprises polynucleotide amplification information.  
     
     
         74 . The system of  claim 58  wherein at least one of the first domain and the second domain comprises genomic information.  
     
     
         75 . The system of  claim 58  wherein the first domain comprises information on a first tissue and the second domain comprises information on a second tissue type.  
     
     
         76 . The system according to  claim 58  wherein at least one of the first domain and the second domain comprises information from a preamplified and amplified sample and providing information from an amplified sample.  
     
     
         77 . The system according the  claim 63  wherein the at least one sample is analyzed for gene expression.  
     
     
         78 . The system according to  claim 58  further comprising a data bank of reference information.  
     
     
         79 . The system according to  claim 78  further comprising obtaining information indicative of a bias within at least one of the first domain and the second domain using the data bank of reference information.