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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