On Dec 2, 2009, at 10:42 AM, Eleni Christodoulou wrote:
Dear list,
I have a couple of questions concerning ridge regression. I am using
the
lm.ridge(...) function in order to fit a model to my microarray data.
Thus *model=lm.ridge(...)*
I retrieve some coefficients and some scales for each gene. First of
all, I
would like to ask: the real coefficients of the model are not
included in
the first argument of the output but in the result of coef(model),
am I
right?
Not exactly. coef(model) extracts the coefficients from the model but
the coefficients do in the example instance I created following the
help page happen to be in the first element of the model.
eg:
> long.rr$coef
GNP Unemployed Armed.Forces Population Year
Employed
25.3615288 3.3009416 0.7520553 -11.6992718 -6.5403380
0.7864825
> long.rr[[1]]
GNP Unemployed Armed.Forces Population Year
Employed
25.3615288 3.3009416 0.7520553 -11.6992718 -6.5403380
0.7864825
Moreover, what does the scale argument represent? Which is its
connection with the coefficients? The R help file os not very
informative
for me...
A plausible response to such a question might be that the help page is
a sketchy substitute for the MASS book. However, I cannot find ridge
regression in the table of contents or in the index of my copy, but I
only have ed. 2 and the current edition is the 4th. So we will both
need to wait for more knowledgeable (or with more recent editions of
MASS) persons to answer that question.
(And "scales" is not an argument, rather it's a returned value.)
Thank you very much in advance,
Eleni Christodoulou
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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