[BioC] [limma] How do I set 'spacing' in lmFit ???

Gordon Smyth smyth at wehi.edu.au
Mon Nov 10 00:02:50 MET 2003

At 03:05 AM 10/11/2003, Marcelo Luiz de Laia wrote:
>Do argument "spacing" refer to spacing in array (membrane) or in datafile?
>Because my datafile is like this:
>In this case, I have one spacing between each gene?

 From a programming point of view, 'spacing' refers to spacing in the data 
file rather than on the array. So, yes, you do have spacing=1 in this case.

The theory behind the statistical method does assume that duplicate spots 
are regularly spaced with respect to physical layout as well, so that the 
correlation between them can be treated as constant across genes, but I 
think it should be close enough to be ok in this application.


> > You can't set duplicates and spacing in this case.  Limma only allows
> > duplicates at regular spacing.
> >
> > Gordon

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