[BioC] normalize.invariantset

Naomi Altman naomi at stat.psu.edu
Sun Mar 26 20:48:04 CEST 2006

When in doubt, copy the function to a new function, edit, and add 
some print statements.  Then you can see what the routine is actually using.

One of the great things about R is that you can see and modify the code.


At 02:45 PM 3/24/2006, Daniel Pick wrote:
>    Thank you very much for this informative reply.
>     Are you sure about this behavior?  I have queried the code contributor
>about this, and he didn't express this definitely.  The latest R Language
>definition (version 2.2.0, dated Oct 6, 2005) does not say that the first
>choice in an argument list is used by default.  In fact, it says that a
>default is specified by setting 'symbol = default' construct, as was done
>with 'verbose = FALSE'  That led me to question the actual behavior of the
>     If you look at the R code for normalize.AffyBatch.invariantset, you
>will see that there are a bunch of 'if' clauses for each baseline type, but
>none of them is set as the default.  So I am really wondering about the
>performance of the call.  It's not at all clear to me that the code behaves
>as you suggest.
>              "James W.
>              MacDonald"
>              <jmacdon at med.umic                                          To
>              h.edu>                    Daniel Pick
>                                        <Daniel.Pick at biogenidec.com>
>              24-Mar-2006 10:51                                          cc
>              AM                        bioconductor at stat.math.ethz.ch
>                                                                    Subject
>              Message Size: 5.0         Re: [BioC] normalize.invariantset
>              KB
>Daniel Pick wrote:
> > Hello,
> >     The Gentleman book suggests to do variant normalizations one should
> > 'normalize(object, method="<some method>").  We would like to know if one
> > selects "invariantset", what does the code use for default settings?  The
> > code for normalize.AffyBatch.invariantset doesn't show a default set, and
> > it seems to indicate that one should specify a baseline type from median,
> > mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly,
> > mmonly, or together.
> > So what does 'normalize(object,method="invariantset") actually do?
>It uses the first option for all arguments that have a character vector
>of choices. For instance, the code says
>function (abatch, prd.td = c(0.003, 0.007), verbose = FALSE,
>      baseline.type = c("mean", "median", "pseudo-mean", "pseudo-median"),
>      type = c("separate", "pmonly", "mmonly", "together"))
>so normalize(object, method="invariantset") will call
>normalize.AffyBatch.invariantset(object, prd.td = c(0.003, 0.007),
>verbose = FALSE, baseline.type = "mean", type = "separate")
>You have to supply an argument for baseline.type and type if you want
>something different.
> >
> > Dan
> >
> > _______________________________________________
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> > Search the archives:
>James W. MacDonald, M.S.
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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