[BioC] Time course....makeConstrasts()

[Khan, Sohail]

Thanks Sean.

My code and the sessionInfo:
Thanks Sean.

Here is my code and sessionInfo.

targets
   FileName Target
1 DF_02.CEL    0hr
2 DF_04.CEL    2hr
3 DF_05.CEL    2hr
4 DF_07.CEL    4hr
5 DF_08.CEL    4hr
> lev <- c("0hr","2hr","4hr")
> lev
[1] "0hr" "2hr" "4hr"
> f <- factor(targets$Target, levels=lev)
> f
[1] 0hr 2hr 2hr 4hr 4hr
Levels: 0hr 2hr 4hr
> design <- model.matrix(~0+f)
> colnames(design) <- lev
> design
  0hr 2hr 4hr
1   1   0   0
2   0   1   0
3   0   1   0
4   0   0   1
5   0   0   1
attr(,"assign")
[1] 1 1 1
attr(,"contrasts")
attr(,"contrasts")$f
[1] "contr.treatment"

> fit <- lmFit(eset, design)
> cont.wt <- makeContrasts(
+ "2hr-0hr",
+ "4hr-2hr",
+ levels=design)
Error in parse(file, n, text, prompt) : parse error

> sessionInfo()
R version 2.1.1, 2005-06-20, i386-pc-mingw32 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  "base"     

other attached packages:
hgu133a2probe   hgu133a2cdf         limma      affydata       affyPLM         gcrma   matchprobes          affy    reposTools       Biobase 
     "1.10.0"      "1.10.0"       "2.0.8"       "1.4.1"       "1.3.3"       "1.1.4"      "1.0.22"       "1.6.7"      "1.5.19"      "1.5.12" 
> 

-Sohail