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

[Gordon K Smyth]

> Hi all,
>
> I see that lmFit have a arguments "spacing".
>
> lmFit(object,design=NULL,ndups=1,spacing=1,correlation=0.75,weights=NULL,met
> hod="ls",...)
>
> In my case, I have ndups=2 (each gene is spoted two times in the filter
> membrane) and my spot layout is:
>
> 03 04 02 04 01
> 05 09 06 10 09
> 08 07 10 01 07
> 06 02 05 08 03
>
> 4x5 (rows x cols)
>
> For example, 03 in position [1,1] is replicate of 03 in [4,5]
>
> In this case, how is the spacing more apropriated for me?

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

Gordon

> Thanks
>
>
> Marcelo Luiz de Laia, M.Sc.
> Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
> Universidade Estadual Paulista - UNESP
> Via de Acesso Prof. Paulo Donato Castelane, Km 05
> 14.884-900 - Jaboticabal, SP, Brazil
> PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
> Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com