[BioC] limma makeContrasts error

[Georg Otto]

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

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