Several different methods can be used to label RNA for array analysis. Cy™ dyes, other fluorophores, or biotin can be incorporated: 1) during the in vitro transcription step of aRNA synthesis, 2) during a subsequent reverse transcription reaction or, 3) after aRNA synthesis in a post-synthesis coupling reaction. Increasingly, amino allyl incorporation combined with a dye coupling reaction is used for the generation of probes for array analysis. This strategy offers several advantages over the direct incorporation of labeled NTPs. Direct incorporation of fluorescently labeled NTPs is inefficient, resulting in lower yields and lower specific activity aRNA. In addition, incorporation efficiency varies for different labels (e.g. Cy3 NTP vs. Cy5 NTP). Because many labeled NTPs are incorporated inefficiently, the cost of producing labeled aRNA can be very high. These problems can be avoided by incorporating an amino allyl UTP into the aRNA and subsequently coupling its reactive amino group to an NHS ester label (e.g. biotin, Cy dye). Unlike dye coupled UTPs, amino allyl modified UTPs are incorporated almost as efficiently as unmodified NTPs and are much less expensive than the dye coupled NTPs. A variety of inexpensive NHS ester dyes and other nonisotopic labels are available from Amersham Biosciences, Pierce Biotechnology, and Molecular Probes.