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: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
****************************************
> 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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