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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 SDRF file, which is a list of comma-separated values in the CSV file format as shown in Figure 2, a column named “Array Design REF” (highlighted in red) lists the array design information for each row in the SDRF file. This allows caArray to associate the correct array design with its corresponding array data files.

When entering the array design information into the SDRF file, please pay attention to the syntax. The correct syntax for most array designs supported by caArray can be found on the NCI instance of caArray at https://array.nci.nih.gov/caarray/home.action. Once you log in, you can click “Manage Array Designs”, click on the array design that your data files use, and capture the value for “Array Design LSID”. Please remove the prefix “URN:LSID:” before you add the array design REF to the corresponding SDRF file column.

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