WE are trying to compare genes expression at different time points to common reference (Ctl) and between each other. This is a targets file: slides Cy3 Cy5 367 96h Ctl 368 48h Ctl 381 48h Ctl 382 96h Ctl 383 48h Ctl 384 96h Ctl 561 12h Ctl 562 12h Ctl 563 12h Ctl 564 24h Ctl 565 24h Ctl 566 24h Ctl This is a code I used: "targets<- readTargets(file="targets.txt") design<- designMatrix(targets, ref="Ctl") design 96h 48h 12h 24h 1 -1 0 0 0 2 0 -1 0 0 3 0 -1 0 0 4 -1 0 0 0 5 0 -1 0 0 6 -1 0 0 0 7 0 0 -1 0 8 0 0 -1 0 9 0 0 -1 0 10 0 0 0 -1 11 0 0 0 -1 12 0 0 0 -1 fit <- lmFit(MA, design, weights = RG$weights) colnames(design) <- c("96h", "48h", "12h", "24h") contrast.matrix <- makeContrasts(96h, 48h, 24h,12h,96h-48h,48h-24h,24h-12h,levels=design) Error: syntax error contrast.matrix <- makeContrasts(96h-48h, 48h-24h, 24h-12h, levels=design) Error: syntax error" What do I do wrong? Thanks. Luda

try "h96", "h48" etc. I think the command doesn't like variable names starting with numbers. -----Original Message----- From: Luda Druskin To: bioconductor@stat.math.ethz.ch Sent: 11/05/04 20:51 Subject: [BioC] limma makeContrasts question WE are trying to compare genes expression at different time points to common reference (Ctl) and between each other. This is a targets file: slides Cy3 Cy5 367 96h Ctl 368 48h Ctl 381 48h Ctl 382 96h Ctl 383 48h Ctl 384 96h Ctl 561 12h Ctl 562 12h Ctl 563 12h Ctl 564 24h Ctl 565 24h Ctl 566 24h Ctl This is a code I used: "targets<- readTargets(file="targets.txt") design<- designMatrix(targets, ref="Ctl") design 96h 48h 12h 24h 1 -1 0 0 0 2 0 -1 0 0 3 0 -1 0 0 4 -1 0 0 0 5 0 -1 0 0 6 -1 0 0 0 7 0 0 -1 0 8 0 0 -1 0 9 0 0 -1 0 10 0 0 0 -1 11 0 0 0 -1 12 0 0 0 -1 fit <- lmFit(MA, design, weights = RG$weights) colnames(design) <- c("96h", "48h", "12h", "24h") contrast.matrix <- makeContrasts(96h, 48h, 24h,12h,96h-48h,48h-24h,24h-12h,levels=design) Error: syntax error contrast.matrix <- makeContrasts(96h-48h, 48h-24h, 24h-12h, levels=design) Error: syntax error" What do I do wrong? Thanks. Luda _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (it.support@wibr.ucl.ac.uk). All files are scanned for viruses.