Hi, I would like to know how to do differential expression analysis in rice affymetrix data?and annotation is done before or after doing differential expression analysis ?

This support site is intended to help people with specific questions about Bioconductor software, rather than as a way for people to teach others how to analyze data.

If you want to learn how to analyze data, there is a worked example by Bernd Klaus and Stefanie Reisenauer that you should read, as well as any number of vignettes for the packages mentioned in that workflow.