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

[Marcelo Luiz de Laia]

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?

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
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