Method for Cross-Instrument Comparison 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.

What is claimed is: 
     
         1 . A method for cross-instrument platform comparison of gene expression data, the method comprising:
 generating first cycle threshold data sets on a first instrument platform, wherein the first cycle threshold data sets are for at least one of a first domain sample, a first domain reference, and a first domain calibrator data set;   generating second cycle threshold data sets on a second instrument platform, wherein the second cycle threshold data sets are for at least one of a second domain sample, a second domain reference, and a second domain calibrator data set;   calculating a first domain ΔC T  given for a first domain sample data set from the first instrument platform given by:
   Δ C   Tfirst   =C   Tq first   −C   Tendo first ,
 
   
       wherein C Tq first  is a threshold cycle for a first domain sample data set, and C Tendo first  is a threshold cycle for a first domain reference data set;
 calculating a first domain ΔC T  given for a first domain calibrator data set from the first instrument platform given by:
   Δ C   Tcb first   =C   Tq cb first   −C   Tendo first ,
 
 
 
       wherein C Tq cb first  is a threshold cycle for a first domain calibrator data set, and C Tendo first  is a threshold cycle for a first domain reference data set;
 calculating a second domain ΔC T  for a second domain sample data set from the second instrument platform given by:
   Δ C   Tsecond   =C   Tq second   −C   Tendo second ;
 
 
 
       wherein C Tq second  is a threshold cycle for a second domain sample data set, and C Tendo second  is a threshold cycle for a second domain reference data set;
 calculating a second domain ΔC T  for a second domain calibrator set from the second instrument platform given by:
   Δ C   Tcb second   =C   Tq cb second   −C   Tendo second ;
 
 
 
       wherein C Tq cb second  is a threshold cycle for a second domain calibrator data set, and C Tendo second  is a threshold cycle for a second domain reference data set;
 calculating a first domain ΔΔC T  for the first instrument platform given by;
   ΔΔ C   Tfirst   =ΔC   Tfirst   −ΔC   Tcb first ,
 
 
 calculating a second domain ΔΔC T  for the second instrument platform given by
   ΔΔ C   Tsecond   =ΔC   Tq second   −ΔC   Tcb second ,
 
 
 determining a measure of preamplifaction or amplification bias within the first domain and within the second domain to produce an indication of bias across the two domains, wherein the measure of measure of preamplifaction or amplification bias is given by,
   ΔΔΔ CT=ΔΔC   T first   −ΔΔC   T second ; and
 
 
 outputting the measure of preamplifaction or amplification bias across the two domains to a view or report of an analysis session. 
 
     
     
         2 . The method of  claim 1 , wherein the first domain sample data set and the second domain sample data set are based on the same target DNA. 
     
     
         3 . The method of  claim 1 , wherein the at least two instrument platforms are polynucleotide amplification instrumentation and microarray instrumentation. 
     
     
         4 . The method of  claim 3 , wherein PCR polynucleotide amplification instrumentation is any of quantitative PCR, real time quantitative PCR, qualitative PCR, and multiplexed PCR. 
     
     
         5 . The method of  claim 3 , wherein the microarray instrumentation is any of a hybridization array, a DNA microchip, or a high-density sequence oligonucleotide array. 
     
     
         6 . The method of  claim 1 , wherein the first domain reference and the second domain reference are each independently an endogenous reference or a passive internal reference. 
     
     
         7 . The method of  claim 1 , wherein the first domain reference and the second domain reference are the same. 
     
     
         8 . The method of  claim 1 , wherein the data obtained from a microarray is converted into a ΔΔCT format using the equation:
 R=(½) ΔΔCT; wherein R is the resulting measurement from the microarray.