Hi Ben,

So (-1,-2,-3,-4) equal to the "mean","median","pseudo-mean","pseudo-median"
arguments used in other normalization methods.

Thanks!
Shuli.
On Tue, Jan 13, 2009 at 12:26 PM, Ben Bolstad <bmb@bmbolstad.com> wrote:

> 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
>
>
> Best,
>
> Ben
>
>
>
> 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.
> >
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> >
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>

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