I am asking for a tool or online software for micoarray analysis (affymetrix) doing the normalization and annotation,online or free trial. i am looking for the different gene expression . would any one help me and guide me please.
As poisonAlien mentioned, a very common toolset would be R with the affy and limma packages. You can go from raw .cel files to statistics with that and also relatively easily annotate the results to your liking.
You are probably looking for something like our arrayanalysis.org which was described here. It uses a.o. the affy and limma Bioconductor packages mentioned by others.
Not sure about such tools (except some CLC paid stuff) or online sw.
But, if you are comfortable with R, there is this great tutorial on how to analyze Affymetrix data. Starting from reading .cel files to getting DEGs and clustering, heatmap, etc. It's fairly simple even if you are new to R.
If your data is from GEO, you can use GEO2R
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