[BioC] limma eBayes: how to determine goodness of fit?

[Paul Shannon]

Hi Mark,

Thanks for the very helpful explanation and -- especially -- the example code.

Two questions remain:

1) You say, "The F-statistic will change since the variances are moderated,  
   causing both the statistic to change and the degrees of freedom to change."
   I am afraid I don't understand this.  In what circumstances does the F-statistic
   change?

2) I am interested in these goodness-of-fit measures because I want to search
   through my data (and the eBayes output) to find genes whose behavior is
   very nicely modeled by different coefficients, like this

        a) devise a variety of model formualae based on biological intuition
           and examinations of the data
        b) fit those models, one at a time
        c) identify different subsets of genes based on their fit to each formula

I remain a bit puzzled by the absence of these statistics from the eBayes output.  Does
their absence suggest that my 3-step procedure (2a-c, above) is not common practice?  And
would _that_ suggest that my 3-step procedure is not such a great idea?  Are there better,
more commonly used ways in limma to look for particular effects and influences
of the experimental factors?

I'll be grateful for any comments or suggestions.

Cheers,

 - Paul