[BioC] limma makeContrasts question

[Stephen Henderson]

try "h96", "h48" etc.

I think the command doesn't like variable names starting with numbers. 

-----Original Message-----
From: Luda Druskin
To: bioconductor at stat.math.ethz.ch
Sent: 11/05/04 20:51
Subject: [BioC] limma makeContrasts question

WE are trying to compare genes expression at different time points to 
common reference (Ctl) and between each other.

This is a targets file:
slides	Cy3	Cy5
367	96h	Ctl
368	48h	Ctl
381	48h	Ctl
382	96h	Ctl
383	48h	Ctl
384	96h	Ctl
561	12h	Ctl
562	12h	Ctl
563	12h	Ctl
564	24h	Ctl
565	24h	Ctl
566	24h	Ctl

This is a code I used:

"targets<- readTargets(file="targets.txt")
design<- designMatrix(targets, ref="Ctl")
  design
    96h 48h 12h 24h
1   -1   0   0   0
2    0  -1   0   0
3    0  -1   0   0
4   -1   0   0   0
5    0  -1   0   0
6   -1   0   0   0
7    0   0  -1   0
8    0   0  -1   0
9    0   0  -1   0
10   0   0   0  -1
11   0   0   0  -1
12   0   0   0  -1

fit <- lmFit(MA, design, weights = RG$weights)

colnames(design) <- c("96h", "48h",  "12h",  "24h")
contrast.matrix <- makeContrasts(96h, 48h, 
24h,12h,96h-48h,48h-24h,24h-12h,levels=design)
Error: syntax error
contrast.matrix <- makeContrasts(96h-48h, 48h-24h, 24h-12h,
levels=design)
Error: syntax error"

What do I do wrong?

Thanks.

Luda

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