Hi all, I have data loaded into an marrayRaw object, and have attached the corresponding marrayInfo object to the targets slot. I would like to run normalization functions on subsets of the marrayRaw object that are selected based on information stored in the targets slot. Is there an easy way to do this, or should I instead create separate marrayRaw objects for each normalization case I am interested in? I'm not clear how the annotation in the targets file will be linked to raw data itself The code I am using currently is: names.sd <- dir(path="c:/docume~1/paul/dev/input/sd", pattern = paste("*", "gpr", sep=".")); nia.layout <- read.marrayLayout(fname = "c:/docume~1/paul/dev/input/GP_M15k1.gal", ngr=4, ngc=12, nsr=25, nsc=26, skip=53, ctl.col=4, pl.col=5); nia.names <- read.marrayInfo (fname = "c:/docume~1/paul/dev/input/GP_M15k1.gal", info.id=4:5, labels=5, skip=53); nia.targets <- read.marrayInfo( fname = 'c:/docume~1/paul/dev/input/annotation.txt'); raw.sd <- read.marrayRaw(fnames = names.sd, path="c:/docume~1/paul/dev/input/sd", name.Gf="F532 Median", name.Rf="F635 Median", name.Gb="B532 Median", name.Rb="B635 Median", layout=nia.layout, gnames=nia.names, targets=nia.targets, skip=29); This raw.sd now has data for control/treated arrays as well as dye- swaps. That meta-information is stored in nia.targets (which is attached in the read.marrayRaw statement), and it is that information that I would like to access for use in normalizations, plotting (i.e. plot all normalized control samples), and other analysis. Hopefully I didn't miss the answer to just this question in the documentation, but please let me know if I should have been able to find it somewhere. Cheers, Paul