Hi. On Wed, May 13, 2009 at 7:19 AM, Lakshmanan Iyer <lax...@gmail.com> wrote:
[snip] > > A question to the developers: > Is it possible to develop a script in R/Perl/Shell so that it will produce > the required directory structure and also print out instruction on moving > the appropriate files (CEL, CDF etc..) to the appropriate directories? I am > afraid to embark on this myself as I live in Linux and Mac world only! I don't see how this can be done generically. Please, note that you do *not* have to copy/move annotation file or data file to the local directory. Instead, it is recommended to keep them all in one place, and *link* to them from you working directory. Also, I keep one working directory per project. On Linux/unix/OSX this is done by: 1. cd my/project/projectA/ 2. ln -s /the/path/to/my/annotationData/ . 3. ln -s /another/path/to/my/rawData/ . On Windows you can achieve the same by using Windows Shortcut links: 1. Open the Windows Explorer and go to your working directory. 2. Open another Windows Explorer and go to the "central" directory contain annotationData/. 3. Right-click and drag the "annotationData/" directory to you working directory and drop it there. This should create a shortcut link such that if you click on it, it will open the "real" directory. The aroma.affymetrix package recognize these shortcuts as well. 4. Do the same for the rawData/ directory. The above cannot be done using an automatic script. Though, if you have a good suggestion how to further simplify how to set up the directory structure or improve the documentation: http://groups.google.com/group/aroma-affymetrix/web/users-guide please let us know. Note that the strict directory structure is there to help you, not to make your life a pain. In think the fact that people on this list can easily troubleshoot others setup problems, is a good illustration why we picked this setup. Imagine trying to do the same with a non-strict directory structure. Finally, if you find yourself using paths (relative or absolute) in your aroma.affymetrix, then you are doing something against the design. Cheers, /Henrik > > Currently, I do this by hand in a unix linux enviroment but for a regular > user this would be helpful. > > -Best > -Lax [snip] --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
