DNA microarray technology has allowed the transcriptome to be studied to a depth that was inconceivable only 10 years ago. Until recently these studies were isolated because, without a universal standard, the results from experiment to experiment and laboratory to laboratory were not directly comparable. For human microarrays, this problem has been addressed by numerous methods, but only two are truly universal. The first method uses genomic DNA as a standard for comparison since it is, by definition, complete and universally available. The second method employs a highly representative total RNA pool such as the one currently available from Stratagene. To determine the advantages and disadvantages of both methods, they were directly compared by hybridization to the University of Texas Southwestern Medical Center's 4000- or 10800-member human cDNA array, using typical microarray techniques. The labeled analytes were 2 microg normal human genomic DNA labeled by nick translation or 20 microg total RNA pool labeled by reverse transcription. The resulting data were then background-subtracted, analyzed, and the number of spots above a background threshold was compared in each sample. Using the McNemar test and a Yate's correction with one degree of freedom, the samples were statistically identical with chi2 = 3.72.