Dear R-Help,

I am using the LIMMA User's Guide 5 January 2007 PDF version.  For the
example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I
could not grasp the rationale in developing the contrast.matrix with
these R statements (">" indicates the R command prompt):

 

> contrast.matrix <-
cbind("CD8-CD4"=c(1,0),"DN-CD4"=c(0,1),"CD8-DN"=c(1,-1))

 

How do we get that numbers (1,0)        (0,1)     and (1,-1)?

 

This knowledge is critical to develop the correct contrasts. I would
like to extend properly this concept to my experiments.

 

Thank you very much.

 

Roger

 

PS. To avoid you going to the LIMMA User's Guide. I show below the
indicated example and R commands used. Please see below.

 

Roger L. Vallejo, Ph.D.

Computational Biologist & Geneticist

U.S. Department of Agriculture, ARS          

National Center for Cool & Cold Water Aquaculture

11861 Leetown Road

Kearneysville, WV 25430

Voice:    (304) 724-8340 Ext. 2141

Email:   roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov> 

 

****************************************

> targets

SlideNumber FileName Cy3 Cy5

ml12med 12 ml12med.spot CD4 CD8

ml13med 13 ml13med.spot CD8 CD4

ml14med 14 ml14med.spot DN CD8

ml15med 15 ml15med.spot CD8 DN

ml16med 16 ml16med.spot CD4 DN

ml17med 17 ml17med.spot DN CD4

 

> design <- modelMatrix(targets, ref="CD4")

Found unique target names:

CD4 CD8 DN

 

> design

CD8 DN

ml12med 1 0

ml13med -1 0

ml14med 1 -1

ml15med -1 1

ml16med 0 1

ml17med 0 -1

 

> fit <- lmFit(MA, design, ndups=2)

 

> contrast.matrix <-
cbind("CD8-CD4"=c(1,0),"DN-CD4"=c(0,1),"CD8-DN"=c(1,-1))

> rownames(contrast.matrix) <- colnames(design)

> contrast.matrix

CD8-CD4 DN-CD4 CD8-DN

CD8 1 0 1

DN 0 1 -1

***************************************************************

 

 

 

 


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