Affymetrix of Santa Clara, Calif., has received US Patent No. 6,858,711, “Labeling reagents.” The invention provides a simplified method for identifying differences in nucleic acid abundances, for example expression levels, between two or more samples. The invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves enzymatically ligating an oligonucleotide to a nucleic acid. For example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.