A similarity matrix is a graphical representation of similar sequences in a data series, and is a matrix of scores that represent the similarity between those data points. Each element or point of the similarity matric contains a measure of similarity between two of the data points. Similarity matrix's are often used to find clusters of data points or to align DNA/gene sequences. The above image is a similarity matrix of differential expression signatures in DNA. Dark red colors indicate high similarity between signatures associated with two contrasts, indicated by the row and column labels. The binary code indicates whether signatures associated with two variables possess a significant level of similarity.
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