[BioC] Accessing Slots in marrayRaw objects

[Paul Boutros]

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