Vassil-

> Do such affy chicken files (correctly formatted for webbioc) exist?

I don't know if they exist as I'm not aware of every annotation  
package available. If they do exist, then you'll have to add them to  
the source code for annaffy.cgi. You should change the following code  
snippet which starts on line 76 to include all the installed  
annotation packages:

		  p(popup_menu('chip', ['hgu133a', 'hgu133b', 'hgu95av2', 'hgu95b',
		                        'hgu95c', 'hgu95d', 'hu6800', 'mgu74av2',
		                        'mgu74b', 'mgu74c', 'rgu34a', 'rgu34b',
		                        'rgu34c', 'rae230a', 'rae230b', 'YEAST'])),

You can get a list of installed annotation packages with the  
following R code:

library(annaffy)
pkgnames <- installed.packages()[,"Package"]
pkgnames[is.annpkg(pkgnames)]

Unfortunately this isn't more automatic or modular.

> If they do not exist is it possible to be created by using the already
> available R modules and packages?

Perhaps, but someone else on the list would be much better suited to  
answer this question.

-Colin
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