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limma design matrix question

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Marcelo Luiz de Laia ▴ 770

@marcelo-luiz-de-laia-377

Last seen 10.2 years ago

Hi All, I have this targets: > ka.rest.targets SlideNumber FileNames Cy3 Cy5 1 1 Ka_Rest_Rep_1.datr Control Treated 2 2 Ka_Rest_Rep_2.datr Control Treated 3 3 Ka_Rest_Rep_3.datr Control Treated and I proceed > design <- designMatrix(ka.rest.targets,ref="Control") > design Treated 1 1 2 1 3 1 > ?designMatrix Is this correct?? I am confused because I read this in help: "There is a need for design matrices for direct two-color design and for single-channel experiments but, this version is only for reference designs." "Examples: targets <- data.frame(Cy3=c("Ref","Control","Ref","Treatment"),Cy5=c("Control","R ef","T reatment","Ref")) designMatrix(targets, "Ref")" In my case, "REF" is my control (Control)? I don't understand the difference between the Reference and Control! 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 21.0 years ago by Gordon Smyth 51k • written 21.0 years ago by Marcelo Luiz de Laia ▴ 770

score 0 · Answer 1 · 2003-11-16

At 06:05 AM 16/11/2003, Marcelo Luiz de Laia wrote: >Hi All, > >I have this targets: > > > ka.rest.targets > SlideNumber FileNames Cy3 Cy5 >1 1 Ka_Rest_Rep_1.datr Control Treated >2 2 Ka_Rest_Rep_2.datr Control Treated >3 3 Ka_Rest_Rep_3.datr Control Treated > >and I proceed > > > design <- designMatrix(ka.rest.targets,ref="Control") > > design > Treated >1 1 >2 1 >3 1 > > ?designMatrix > >Is this correct?? Yes. >I am confused because I read this in help: > >"There is a need for design matrices for direct two-color design > and for single-channel experiments but, this version is only for > reference designs." >"Examples: > targets <- >data.frame(Cy3=c("Ref","Control","Ref","Treatment"),Cy5=c("Control"," Ref","T >reatment","Ref")) > designMatrix(targets, "Ref")" > >In my case, "REF" is my control (Control)? > >I don't understand the difference between the Reference and Control! In the function designMatrix(), the "reference" is any RNA source which appears on all the arrays and which therefore acts as a "common reference". Your "Control" sample obviously fits this criterion. You have a simple replicated experiment. This can be viewed both as a direct design and as a reference design. Anything works fine for this simple design. 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 >---