http://chipster.csc.fi/ has microarray tools based on Bioconductor packages like Limma and friends that may suit some of your needs. I believe a VM image is available to simplify installation if you want to try it out painlessly.
Please review the other Public servers available for one option (these update frequently). Search on the wiki for "microarray" to start with:
Some of those tools may be in the ToolShed for local/cloud use, permitting you to scale up dedicated resources as needed:
And if you have programming experience or resource where you are working, almost any tool your prefer could be wrapped and added to use within Galaxy. (And please consider sharing, contributions to the ToolShed are always welcomed!):
Best, Jen, Galaxy team
Like mentioned in the previous answer, Chipster is available as a VM image which contains all the analysis tools and reference data. Note that we offer evaluation accounts to our Chipster server, as people often want to try the software before downloading it (the VM is quite large because of all the aligner index files etc).
Best, Eija, Chipster team