Dear BioC, For FREE of cost, anyone can UPLOAD and ANALYZE microarray data, [ Overview of ArrayQuest system].(looking for LIMMA method to add in to our METHOD DATABASE) http://proteogenomics.musc.edu/quickSite/arrayQuest.php?page=home&act= manage&process=Login Steps/Structure of ArrayQuest: 1. Create your project (microarray project) a. you can upload your data (your data can not be viewed by anyone else, unless if you want to..if you have alrady stored your data in to MUSC microarray repository, can goto Step2) 2. Select Method from Method Database: Analysis method, which is R SCRIPTS currently using all BioC libraries and functions. ***Anyscript script can be used to analyze ANY GENOMIC Data.e.g, PERL,Javascript,SOAP,Unix Shell Script*** a. please read method description before you make a decision which method is suitable for your analysis. b. please read method parameter description (what method requires, howmany CEL files, or FDR threshold..) 3. Build your database : (you can use your own uploded data or you can search MUSC microarray database to get your data) 4. Choose your dataset: You can choose your uploaded data or you can choose few files from your dataset a. use of step4 is for flexibility. e.g., Sometimes, user wants to use only 5 CEL files out of 10 CEL files uploaded. 5. Run your analysis: (upon completion you can get an email with resulting link or you can monitor your analysis) Please, let me now if you have any questions..I am looking for LIMMA method to add in to our METHOD DATABAESE, if anyone interested, please let me know..we can be in touch, Sorry for sending this again, I think privious message was a formated wrong. Saurin