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.
- Location of annotation data files, e.g. CDF, ACS, UFL, ... [VOLUNTEERS: Remove/Create deprecated subpage for dChip annotation files]
- Location of raw data files, e.g. CEL files.
- Quick Summary Of Required File Structure
The How tos section on how to use cross-platform supported links for setting up directory structures linking to data sitting elsewhere.