[BioC] normalize help revisted

Rafael A. Irizarry ririzarr at jhsph.edu
Mon Sep 29 13:46:25 MEST 2003


for the last release of affy (1.2.x) i followed, as best i could, your
recommendations for documenting the normalize method. 

with the latest R im getting the following warning

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object

if i put an alias for normalize in this documentation object, as suggested
by R check, then the help for  normalize will once again become affy

the problem is that the "usage" for normalization in affy is
"normalize(object,...)" but if i put that in the help file for the affy
specific normalization documentation i get the above warning. for now, im
simply removing "normalize(object,...)" from the usage section since it is
described in the details section. this seems to have gotten rid of the 
warning and i dont think the help file lost much. but, if you have any 
suggestions please let me know.


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