Setup: Location of raw data files

CEL files

Raw data is special in the sense that it should be considered read only, that is, we do not plan to update the raw data files after being obtained. The package looks for raw data sets in directory rawData/ in the current working directory.

Example:

Here is an example of a CEL data set "SinclairA_etal_2006" (no tags) for the 500K chip set:

rawData/SinclairA_etal_2006/

  Mapping250K_Nsp/
    01,XX,2006-07-12.cel
    02,XY,2006-07-14.cel
    ...
    10,XX.cel
    C1.cel 02,XY,2006-07-12.cel

  Mapping250K_Sty/
    01,XX,2006-07-19,2nd.cel
    02,XY,2006-07-20.cel
    ...
    10,XX.cel
    C358,control.cel

Note that the above two array sets have samples "01", "02", ..., "10" in common, whereas sample "C1" was only hybridized to the Nsp chip and sample "C348" was only hybridized to the Sty chip. Regardless of chip type, the data has samples "01", ..., "10", "C1", and "C358".