With the affydata package installed, data(Dilution) loads an AffyBatch
instance "Dilution"; Dilution[,1:3] is a three-chip subset; the class is
closed under the subsetting operation so this yields a valid AffyBatch.  The
interpretation of "[,]" applied to AffyBatch instances should be intuitive
_for indices provided to the right of the comma_.  If you have something to
the left of the comma, you will get a warning; there the interpretation is
not intuitive but reflects ancient legacy.  If you are seeing something
different provide all details.

On Fri, Nov 20, 2009 at 5:48 AM, Thomas Hampton <
Thomas.H.Hampton@dartmouth.edu> wrote:

> Using read.affy() one ends up with an AffyBatch, a complex R structure. If,
> at that point, you decide
> you want to run RMA on a subset of the chips you just read in, things get
> tricky -- you are definitely
> not dealing with a matrix whose columns you can simply reference at will.
>
> In the past, I have dealt with this by simply starting over. This makes me
> feel like sort of an idiot.
>
> Is there a nice way to create a modified AffyBatch containing only the
> chips I want?
>
> Thanks.
>
> Tom
>
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