[BioC] Baseline selection methods used in normalize.scaling?

Henrik Bengtsson hb at stat.berkeley.edu
Mon Jan 12 19:45:05 CET 2009

More of a general help; have a look at the aroma.affymetrix package


which doesn't have memory limits.


On Mon, Jan 12, 2009 at 7:43 AM, shuli kang <kangshuli at 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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