How to: Migrating all or parts of a project to another file system

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Briefly describe how aroma.* reads data from one directory and outputs in another (give one or two examples and show how the directories can be located).
rawData/: The raw data sets must be copied.
annotationData/: Of course, the annotationData/ directories also have to be available on the new machine, e.g. via copying. Don't forget about the *,monocell.CDF files; these are created automatically from the main *.CDF file, so it is not a problem if forgotten, but it take quite some time (10-60 minutes) to build them so it is worth copying.
Show how the data directories/files can be copied, preferable using R (see copyDirectory()/copyFile() in R.utils). What files to include (there are some files starting with a period (.), which is by default not listed on Unix systems using ls (you need ls -a to see them).
(Optional): By copying some o the cache files under ~/.Rcache/aroma.affymetrix/ one can save additional processing time on the destination system.

HB 2009-11-13

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First of all, make sure to read the 'Migrate and reproduce an analysis elsewhere' how to page

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