I did a quick search in the forum and MeV manual .pdf and didn't find any info on loading Nimblegen data. Is there a way to edit my data files so that I can upload them in either Affy RMA format or anything else that works? Possibly not. Sorry if I've overlooked something obvious, this is my first foray into microarray analysis…
Please take a look at under the "data" folder of MeV, where we have various sample files of various formats that we support.
We do not support Nimblegen and I am not familiar with it either. But if you can get your data in any of the formats that corresponds to a file loader you can load any data. Also if can email us an example file structure we can make a little specific suggestion.
Also note for un-supported arrays the user has to provide annotation if its required..
Hope it helps,