[BioC] normalize.invariantset

Daniel Pick Daniel.Pick at biogenidec.com
Fri Mar 24 00:33:47 CET 2006


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?

Dan



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