Hierarchical clustering of replicate datasets generated by direct labeling, IVT and R-PCR. Each thin bar represents a single datapoint. Red bars correspond to enrichment in the Cy5-labeled Alu I probe, while green bars correspond to enrichment in the Cy3-labeled Rsa I probe. The dendrograms (top) indicate clustering relationships among the sample replicates. The lengths of the branches represent the degree of similarity between the samples (shorter indicates higher similarity). Purple stripes to the right of the diagram highlight discordant areas (log ratios with opposite signs) in the R-PCR replicates relative to the direct labeling and IVT samples.