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All aroma.* packages are designed to have data files located in specific directories following a strict directory structure.

Fundamental to Affymetrix data analysis is CEL and CDF files. A CEL file is a so called data file, which contains the observed signals, whereas a chip-definition file (CDF) is a so called annotation file, which contains information about the layout of a specific chip type. In order to minimize the number of arguments specified by the user, aroma.affymetrix looks for annotation files in pre-defined directories as described next.

See also

The How tos section on how to use cross-platform supported links for setting up directory structures linking to data sitting elsewhere.