Setup: Quick Summary Of Required File Structure

A typically directory structure of an aroma.* project looks like this:

<current working directory>
  +- annotationData/
  |  +- chipTypes/
  |     +- <chipTypeA>/ <-- must match exactly the name of the CDF file (fullname minus tags)
  |     |  +- CDF file(s) and other annotation (possibly subdirectories)
  |     |
  |     +- <chipTypeB>/ <-- must match exactly the name of the CDF file (fullname minus tags)
  |        +- CDF file(s) and other annotation (possibly subdirectories)
  |        ...
  |
  +- rawData/
  |  +- <dataSet1>/
  |  |  +- <chipTypeA>/ <-- must match exactly a chip type folder under annotationData/
  |  |     +- CEL files
  |  |
  |  +- <dataSet2>/
  |  |  +- <chipTypeB>/ <-- must match exactly a chip type folder under annotationData/
  |  |     +- CEL files
  |  |
  |  +- <dataSet3>/
  |  |  +- <chipTypeA>/ <-- must match exactly a chip type folder under annotationData/
  |  |     +- CEL files
  |  ...

You must follow this structure/format exactly include the case of letters. For instance, 'GenomeWideSNP_6' is not the same as 'genomewidesnp_6'. Below, <...> indicates a name of folder or file that you must supply according to your project/computer/chip type etc.

Example

Here is a complete directory structure with annotation data and two data sets. For other chip types and further details, see the Setup section.

C:/Documents and Settings/JoeD/My Documents/ProjectA/
  +- annotationData/
  |  +- chipTypes/
  |     +- Mapping50K_Hind240/
  |     |  +- Mapping50K_Hind240.cdf
  |     |  +- Mapping50K_Hind240,monocell.cdf
  |     |  +- Mapping50K_Hind_probe_tab
  |     |  |
  |     |  +- dChip/
  |     |  |  +- 50k hind genome info AfAm june 05 hg17.xls
  |     |  |  +- Mapping100K_Hind snp info.txt
  |     |  |
  |     |  +- NetAffx/
  |     |     +- Mapping50K_Hind240_annot.csv
  |     |
  |     +- Mapping250K_Nsp/
  |     |  +- Mapping250K_Nsp.cdf
  |     |
  |     +- Mapping250K_Sty/
  |        +- Mapping250K_Sty.cdf
  |
  +- rawData/
     +- SinclairA_etal_2006/
     |   +- Mapping250K_Nsp/
     |   |  +- 01,XX,2006-07-12.cel
     |   |  +- 02,XY,2006-07-14.cel
     |   |  +- ...
     |   |  +- 10,XX.cel
     |   |  +- C1.cel
     |   |
     |   +- Mapping250K_Sty/
     |      +- 01,XX,2006-07-19,2nd.cel
     |      +- 02,XY,2006-07-20.cel
     |      +- ...
     |      +- 10,XX.cel
     |      +- C358,control.cel
     |
     +- Yu50K
        +- Mapping50K_Hind240/
           +- XYZ0001.cel
           +- XYZ0002.cel
           +- XYZ0003.cel
           +- XYZ0004.cel
           +- XYZ0005.cel