[BioC] limma makeContrasts error

[James W. MacDonald]

Georg Otto wrote:
> Dear Bioconductors,
> 
> I have a problem defining a contrast using the function makeContrasts
> in LIMMA. It seems to me as if my problem has to do with the way the
> function deals with groups with names that contain digits and
> literals. There was a simmilar question in this mailing list in
> January, but as far as I can see it never got answered.
> 
> I have a time course experiment containing different time points,
> including 6hpf and 12hpf. Generating a contrast to get differentially
> expressed genes between those two time points results in an error:
> 
> 
>>cont.matrix<-makeContrasts(contrast=12hpf-6hpf, levels=design)
> 
> Error: syntax error
> 
> Quoting the time points results in a different error:
> 
> 
>>cont.matrix<-makeContrasts(contrast="12hpf"-"6hpf",levels=design)
> 
> Error in "12hpf" - "6hpf" : non-numeric argument to binary operator

I don't think you can use makeContrasts() with names that start with 
numbers (I certainly have never been able to). You can either change the 
names to hpf12 and hpf6, or make the contrasts matrix by hand.

Best,

Jim


> 
> For several reasons I do not want to change the names of the groups,
> therefor I would be very grateful for a hint how to deal with these
> group names.
> 
> I am using limma 2.0.7 and R 2.1.0
> 
> Thanks a lot!
> 
> Georg
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623