How to deal with .CEL files in GRN reconstruction

Question

[Parisa]

My goal is to reconstruct a Gene Regulatory Network (GRN) from a set of data downloaded from GEO repository. I have downloaded CEL files from GEO and need to somehow make a single expression dataset from them (to use as the input of "clr" function). I am not sure how I can make that dataset. I tried to compute expressions measure by using "justRMA", but the output object is kind of unfamiliar for me. Any instruction, suggestion, or help in understanding the data format can help me a lot.

Appreciate it.

Thanks

[zizigolu]

few months ago i did like so,

i downloaded some CEL files from GEO, normalized them with RMAExpress, then i installed geworkbench on my windows OS and uploaded the normalized txt file and finally i run ARACNe from geworkbench...the result were some probes that i annoatated them