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

Ben Bolstad bmb at bmbolstad.com
Tue Jan 13 05:26:57 CET 2009

Apologies for not having this documented anywhere and having not looked
at the code in way too long I had completely forgotten what these were
myself. But digging around in the C code:

 ** int baseline - index of array to be used as baseline. 
 **                this will be 0..cols-1, if  it is 
 **                -1 pick array with median overall (total) intensity
as baseline
 **                -2 pick array with median median as baseline
 **                -3 generate a probewise median array for baseline
 **                -4 generate a probewise mean array for baseline



On Mon, 2009-01-12 at 23:43 +0800, shuli kang 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.
> 	[[alternative HTML version deleted]]
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