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

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Marcelo Luiz de Laia ▴ 770

@marcelo-luiz-de-laia-377

Last seen 10.2 years ago

Hi all, I see that lmFit have a arguments "spacing". lmFit(object,design=NULL,ndups=1,spacing=1,correlation=0.75,weights=NU LL,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. Bioqu?mica 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@yahoo.com ---

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ADD COMMENT • link updated 21.1 years ago by Gordon Smyth 51k • written 21.1 years ago by Marcelo Luiz de Laia ▴ 770

score 0 · Answer 1 · 2003-11-08

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Gordon Smyth 51k

@gordon-smyth

Last seen 4 minutes ago

WEHI, Melbourne, Australia

> 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. Bioqu?mica 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@yahoo.com

ADD COMMENT • link 21.1 years ago Gordon Smyth 51k

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Hi, Do argument "spacing" refer to spacing in array (membrane) or in datafile? Because my datafile is like this: Name Gene1(1) Gene1(2) Gene2(1) Gene2(2) (...) In this case, I have one spacing between each gene? Thanks Marcelo > You can't set duplicates and spacing in this case. Limma only allows > duplicates at regular spacing. > > Gordon > ---

ADD REPLY • link 21.1 years ago Marcelo Luiz de Laia ▴ 770

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At 03:05 AM 10/11/2003, Marcelo Luiz de Laia wrote: >Hi, > >Do argument "spacing" refer to spacing in array (membrane) or in datafile? > >Because my datafile is like this: > >Name >Gene1(1) >Gene1(2) >Gene2(1) >Gene2(2) >(...) > >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. Regards Gordon >Thanks >Marcelo > > > > You can't set duplicates and spacing in this case. Limma only allows > > duplicates at regular spacing. > > > > Gordon

ADD REPLY • link 21.1 years ago Gordon Smyth 51k