[BioC] [maSigPro] get.siggenes, PlotGroups - results

[Maciej Jończyk]

Dear List Members

I'd like to make sure I understand results of
"get.siggenes" correctly.

I've make model with degree=4 and I get following coefficients (with my
interpretation):

beta0 (intercept component for control)
betacoldvsctrl (intercept component for cold vs control)
betaczas (linear component for control)
betaczasxcold (linear component for cold)
betaczas2 (quadratic component for control)
betaczas2xcold (quadratic component for cold)
...
and so on to four order.

And in sig.pvalues there are corresponding p-values.

Is it right?

I also have question regarding plots generated by PlotGroups.
Here one can use step.method option to obtain regression curve. Possible
values are the same as in T.fit, so I suppose that if I use the same
method in both T.fit and PlotGroups I'll get proper regression curve.
The problem is that curve sometimes fit bad to points (examined by eye).
Is it because of low R-square threshold (I used 0.60)?
Or is it because not all variables are selected in regression?

Any help will be very appreciated. I'd like to use this results in my
Ph.D thesis.

Best regards,

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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