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If more than one array design is selected, and if the data and sample annotations are in the MAGE-TAB format, additional information needs to be provided in the form of a SDRF metadata file in the CSV file format. In the SDRF file, which is a list of lists all the experiment's samples as shown in Figure 2 below, a column named “Array Design REF” (highlighted in red) shows the array design reference for each sample, as shown in Figure 2 below. This allows caArray to associate the correct array design with its corresponding array data files.

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