[BioC] Limma error message

[Richard Friedman]

Dear Bioconductor List,

I am using limma to fit a linear model with what
I believe is called a disconnected design:


 > data <- ReadAffy()
 > eset<-rma(data)
 > design<-model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4)))
 > colnames(design)  
<- 
c("1A_L5V4_No_Pon_A","1C_L5V4_Pon_A_DHT_24hrs","2A_L5S2_No_Pon_A","2C_L5 
S2_Pon_A_DHT_24hrs")
 > fit<-lmFit(eset,design)
 > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs  
-2A_L5S2_No_Pon_A -1C_L5V4_Pon_A_DHT_24hrs  
+1A_L5V4_No_Pon_A,levels=design)

I get the error message:

Error: syntax error in "  
contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs"

I would greatly appreciate any suggestions.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, John Stewart Williamson