[BioC] normalize.invariantset

lgautier at altern.org lgautier at altern.org
Fri Mar 24 13:56:29 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,

What do you mean by "default set" ?
What you write below suggests that the issue is about
"default parameters".

>                                                                      and
> it seems to indicate that one should specify a baseline type from median,
> mean, pseudo-median, and pseudo-mean,

This is what the code says.

> and a type from separate, pmonly,
> mmonly, or together.

This relates to the type of methods for dealing with Perfect Match (PM)
and Mismatch (MM) probes.
(Which is convenient, is nicely unified accross normalization methods in
affy, and was added by Ben Bolstad if I remember it correctly... and I
suspect he added the baseline type as well).

> So what does 'normalize(object,method="invariantset") actually do?

Did you already check either the help page
for the function 'normalize.AffyBatch.invariantset', or a manual on how R
is dealing with default parameters in the signature of a function ?

Hoping this helps,


> Dan

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