TM4 is an open source microarray data analysis tool: http://www.tm4.org/

There are also extensive tools for microarray analysis in the Bioconductor package for the R statistics language. They are completely free, but require you to be comfortable using a command line and exercising a bit of programming logic.

Here is a good starting point with R and Bioconductor: https://www.biostars.org/p/53870/

According to my experience R and Bioconductor would be best as pointed by Mr. Miguel, I would recommend to take this tutorial it helped me a lot with my Agilent and Affymetrix data both.

http://wiki.bits.vib.be/index.php/Analyze_your_own_microarray_data_in_R/Bioconductor

Hello Abdullah,

In my opinion best way to analyze Affymetrix microarray data would be R+Bioconductor. However if you want to get results fast you can use TAC and EC both provided for free by Affymetrix. It is a trade of becouse with R you can do anything but you need to know about programming in R. On the other hand with TAC+EC you dont have to have any programming skills but you can do much less with results.