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

Paul Shannon pshannon at systemsbiology.org
Fri Jun 1 15:19:12 CEST 2007

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

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.


 - Paul

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