[BioC] normalize.invariantset

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 24 19:51:44 CET 2006

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.



> Dan
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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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