[BioC] normalize.invariantset

[Daniel Pick]

Hi,
   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
call.
    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.

Dan


                                                                           
             "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   
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Daniel Pick wrote:
> Hello,
>     The Gentleman book suggests to do variant normalizations one should
do
> 'normalize(object, method="<some method>").  We would like to know if one
> selects "invariantset", what does the code use for default settings?  The
R
> 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.

HTH,

Jim


>
> Dan
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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