1. A computer implemented method comprising: analyzing quantitatively concordance between two or more microarray data sets, wherein the two or more microarray data sets comprise data from independent microarray experiments based on a plurality of replicate microarray chips, and wherein said analyzing step comprises: (1) updating chip definition files in each of the two or more microarray data sets, wherein the updating comprises scanning the chip definition files into a computer memory; and using a computer processor to compare information from the chip definition files with updated information for chip definition files, and to update a relationship between probes, probe sets, and gene definitions in each of the two or more microarray data sets; (2) evaluating outlier probe values in each of the two or more microarray data sets using a computer processor, wherein the evaluating comprises: (i) applying data transformation on each of the two or more microarray data sets to satisfy underlying assumptions for statistical analysis, wherein the assumptions for statistical analysis are normality of error variance and homogeneity of error variance across the range of signal intensities; (ii) applying data normalization to correct for global differences in fluorescence levels among microarray chips, (iii) removing data from replicate microarray chips from the analysis that contain a percentage of outlier probe values for that microarray chip greater than a defined threshold, (iv) reiterating steps (i)-(iii) whenever the data from a replicate microarray chip is removed in step (iii) until there are no more chips with a percentage of outlier probe values above the defined threshold, and (v) masking the data on all remaining microarray chips by removing from further analysis the values of all replicates of probes that include at least one outlier; (3) determining a gene expression score for the remaining probes of each probe set in each of the two or more microarray data sets; (4) evaluating treatment effects by performing a statistical analysis of gene expression scores between two or more groups in each of the two or more microarray data sets; and (5) determining concordance between the two or more microarray data sets.