Figure 3.

Examples of the Gecko agglomeration syntax. a) Concatenate: concatenation of a large number of scans (here arising from many samples, each profiled across three distinct chip designs) into a single data matrix; normalizations are computed on-the-fly; b) Cat Ratio: element-by-element ratios are computed for two data matrices, creating a new data matrix containing ratios and P-values; c) Combine on Columns: the columns of two data matrices are concatenated to create a larger data matrix; d) Reduce on Qlist and Reduce on Columns: a data matrix is subsetted on its rows (right-hand arrow) or on its columns (bottom arrow), respectively, to form reduced data matrices; e) Merge Replicates: replicates are merged by taking medians of intensities (with concomitant reestimation of noise terms); f) Join: two data matrices are joined using qualifiers (row indices) as the join key.