Hello,when I download the .cel files from the [Broad CMAP][1] and open them, what I see is just digital gibberish.So I download the software called Gene Expression from the Aff company.

However,there are three algorithm named RMA,MAS5,PLIER WorkFlow to choose and the results are different when choosing different algorithm.

So which algorithm should I choose? And what difference are the three algorithm?

 [1]: http://www.broadinstitute.org/cmap/cel_file_chunks.jsp
Run the RMA method.

See: http://bmbolstad.com/misc/ComputeRMAFAQ/ComputeRMAFAQ.html