Unsupervised hierarchical clustering of 42 murine U74Av2 Affymetrix arrays. Unsupervised hierarchical clustering of 42 murine U74Av2 Affymetrix arrays shows that probe synthesis and hybridization is not a major source of experimental variability. Expression profiles shown were from three different experimental groups; one using cultured murine myogenic cells (VSM samples), one using mouse spleens (KNagaraju samples), and one group from mouse skeletal muscle from normal and mdx mouse strains (FBooth samples). For the KNagaraju samples, the same spleen RNA was split prior to cDNA synthesis to create duplicate cDNA-cRNA-profile results; these duplicates show a very high correlation coefficient, and close relationship by Unsupervised clustering (low branches on dendrogram). The VSM cultured samples were each derived from different culture plates, and the FBooth samples from different murine muscles. The duplicate murine muscle samples are more closely related (high correlation coefficient) than the parallel cultures (VSM). Additional variables, such as male versus female (KNagaraju samples), and time after TSA treatment (VSM samples) are indicated, but are not relevant for this manuscript, and will be discussed in more detail elsewhere.