Hi Umme,
With a little experience that I have I can tell you that you can get more
information here at

http://www.bioconductor.org/packages/2.6/bioc/vignettes/simpleaffy/inst/doc/simpleAffy.pdf
>From the above file it tells that covdesc is default file. In page 3 you can
see how the file looks, this file describes your cell files. You can
understand more by reading above file.
Coming to where to store this file, You can store the data in any directory
but only specify where the file is stored.
If using the Rgui
(use \File -> Change Dir"menu item).

otherwise commands like setwd() can help  you are set the working directory.

Hope this helps,

Regards,

Viritha

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