[BioC] LIMMA makeContrasts(Groups[1]-Groups[2], levels = design) Error

[Saurin D. Jani]

Hi BioC,

I have question about LIMMA makeContrasts( ) function. I am reading parameter
file for LIMMA from out side R environment and building design matrix.

G1 G2 and G3 are Group names coming from parameter file.  

> Groups <- c("G1","G2","G3");
> colnames(design) <- c(Groups);
> design
  G1 G2 G3
1  1  0  0
2  0  1  0
3  0  1  0
4  0  0  1
5  0  0  1
6  0  0  1
attr(,"assign")
[1] 1 1 1
attr(,"contrasts")
attr(,"contrasts")$"factor(c(mask))"
[1] "contr.treatment"

> fit <- lmFit(myRMA,design);

upto here it works great. now, when I do, 

> makeContrasts(Groups[1]-Groups[2],levels  = design);
Error in Gs[1] - Gs[2] : non-numeric argument to binary operator


has anyone came across this sort of problem? or may be I am doing something
wrong..? 

any suggestions?


Saurin




-- 
|------------------------------------------------
| Saurin Jani,MS
| Statistical and Research Analyst
|
| Department of Cell Biology and Anatomy
| Medical  University of South Carolina (MUSC)
| 173 Ashley Ave
| Charleston,SC - 29407 (US)
| 
| Email: jani at musc.edu
| Phone: (843)792-5483
|------------------------------------------------