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

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

Note that this is an R thing, I think - variable names cannot begin with a number Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W. MacDonald Sent: 08 September 2005 16:22 To: Georg Otto Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] limma makeContrasts error 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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor