[BioC] Limma error message

[Francois Pepin]

Hi Richard,

the problem is with the names of your samples.

Limma treats the sample names as R variables when it makes the contrast,
and R variables cannot start with digits.

Just add a letter in front when setting the colnames of the design
matrix and when doing the contrast and it should get rid of the error.

Francois

On Wed, 2007-04-11 at 17:58 -0400, Richard Friedman wrote:
> 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
> 
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