Hi, I am trying to make some contrasts in limma. I keep getting a syntax error. My design is read in ok, as well as everything else upto making a contrast matrix. design 4day 9day 14day 19day 14daf 19daf 4daf 9daf control 1 -1 0 0 0 0 0 0 0 0 2 -1 0 0 0 0 0 0 0 0 3 -1 0 0 0 0 0 0 0 0 4 -1 0 0 0 0 0 0 0 0 5 0 -1 0 0 0 0 0 0 0 6 0 -1 0 0 0 0 0 0 0 7 0 -1 0 0 0 0 0 0 0 ....42 arrays. contrast.matrix <- makeContrasts(4day,9day,14day,19day,14daf,19daf,4daf,9daf,control,4day -19day,levels=design) Error: syntax error What am I doing wrong? thanks Simon. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 909 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040113/667ce7b7/attachment.bin

In R, variables are not allowed to have names with start with numbers. This affects the makeContrasts() function. Please choose colnames for your design matrix which do not start with numbers. Try make.names(colnames(design)) to see whether R considers your colnames to be valid variable names. Gordon At 08:38 AM 14/01/2004, Simon Melov wrote: >Hi, >I am trying to make some contrasts in limma. I keep getting a syntax >error. My design is read in ok, as well as everything else upto making a >contrast matrix. > >design > 4day 9day 14day 19day 14daf 19daf 4daf 9daf control >1 -1 0 0 0 0 0 0 0 0 >2 -1 0 0 0 0 0 0 0 0 >3 -1 0 0 0 0 0 0 0 0 >4 -1 0 0 0 0 0 0 0 0 >5 0 -1 0 0 0 0 0 0 0 >6 0 -1 0 0 0 0 0 0 0 >7 0 -1 0 0 0 0 0 0 0 > >....42 arrays. > >contrast.matrix <- >makeContrasts(4day,9day,14day,19day,14daf,19daf,4daf,9daf,control ,4day-19day,levels=design) > >Error: syntax error > >What am I doing wrong? > >thanks > >Simon.