Hi Henrik,

Thanks for your suggestion.  This package is just what we need.

Shuli.
On Tue, Jan 13, 2009 at 2:45 AM, Henrik Bengtsson <hb@stat.berkeley.edu>wrote:

> More of a general help; have a look at the aroma.affymetrix package
>
>  http://www.braju.com/R/aroma.affymetrix
>
> which doesn't have memory limits.
>
> /Henrik
>
> On Mon, Jan 12, 2009 at 7:43 AM, shuli kang <kangshuli@gmail.com> wrote:
> > Hi,
> >
> > I'm using the normalize.scaling function in the affyPLM package to
> normalize
> > the data from several chips.  By default, the argument "baseline" was set
> as
> > "-1".  The document says negative values control different baseline
> > selection methods:
> >
> > baseline Index of array to use as baseline, negative values (-1,-2,-3,-4)
> > control different baseline selection methods
> >
> > But I can't find detailed description of these methods anywhere.  Could
> > anyone tell me what these methods are actually?
> >
> > PS: I'm dealing with plenty of chip data now.  Usually I read all the CEL
> > files at one time.  However, I have to read them one by one if too many
> CEL
> > files involved, due to the limited physical memory .  In such cases, I
> tried
> > to manually select the same reference array as the one selected by the
> > default "baseline" values.  So I want to know more about these reference
> > selection methods.   Of course, I could always choose the first array as
> a
> > reference. But this seems too arbitrary?
> >
> > Thanks in advance!
> >
> > Shuli.
> >
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> >
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