I have a large amount of Agilent data (580 text files that are ~200 MB in size each) that I'd like to normalize. I've run into a problem in that my machine (with 8 GB of memory) still runs out of memory when I try to read the files using marray in order to geneerate an expression set for normalization. I don't need the expression set, just the normalized output--is there an analogous program for Agilent data like justRMA is used for Affy data?
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You might want to consider using a one-sample-at-a-time normalization scheme like frozenRMA: http://www.bioconductor.org/packages/2.11/bioc/html/frmaTools.html