•Target DNA binds non-specifically and yields background
noise
•Labeling procedure is inherently inefficient and 90% of
target is lost in process
•Uniform hybridization temperature used to decouple
non-homologous targets from probes fails to account for variations in
target-to-probe binding energies
•
•Insensitive to subtle changes in gene expression (<
1.5-fold)
•Requires large, expensive equipment and is arduous
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