Hi, I'm trying to analyze a time series experiment consisting of 2 conditions (stimulated and mock) with three time points (12,16, 24 hours) with 3 replicates at each condition. Although I am specifying the time points, groups, and conditions explicitly, the "plotProfile" function does not seem to correctly assign the data which makes me worried that the data is also not being correctly analyzed in mb.long(). Any suggestions? I must be misinterpreting something in the documentation. Here is self-contained toy example: library(timecourse) # List of arrays. arrays <- c("BR_12_1.CEL","BR_12_2.CEL","BR_12_3.CEL","BR_16_1.CEL","BR_16_2.CEL ","BR_16_3.CEL","BR_24_1.CEL","BR_24_2.CEL","BR_24_3.CEL","Mock_12_1.C EL","Mock_12_2.CEL","Mock_12_3.CEL","Mock_16_1.CEL","Mock_16_2.CEL","M ock_16_3.CEL","Mock_24_1.CEL","Mock_24_2.CEL","Mock_24_3.CEL") # Set up the groups. c.grp <- c("BR","BR","BR","BR","BR","BR","BR","BR","BR","Mock","Mock","Mock","M ock","Mock","Mock","Mock","Mock","Mock") t.grp <- c(12,12,12,16,16,16,24,24,24,12,12,12,16,16,16,24,24,24) r.grp <- c("BR12","BR12","BR12","BR16","BR16","BR16","BR24","BR24","BR24","M12" ,"M12","M12","M16","M16","M16","M24","M24","M24") # Fake data on two genes. gene1 <- c(9.040573,9.149422,9.105320,10.943353,10.923959,10.064324,13.005580,1 3.042221,13.649432,8.299019,8.222491,8.106000,7.986045,8.041965,8.2224 59,8.601860,7.814944,8.373308) gene2 <- c(12.240573,12.049422,12.095320,12.843353,12.993959,13.164324,12.90558 0,13.142221,13.349432,8.199019,8.022491,8.006000,7.786045,8.241965,8.5 22459,8.301860,7.614944,8.173308) # Create the data matrix. data <- as.matrix(rbind(gene1,gene2),colnames=arrays) colnames(data)=arrays # Set up the time points and number of conditions. nTimePoints <- 3 # T = 12, 16, 24 hours nGenes <- 2 # genes nCond <- 2 # BR, Mock size <- matrix(nTimePoints, nrow=nGenes, ncol=2) MB.2D.BR <- mb.long(data, method="2D", type="none", times=nTimePoints, reps = size, condition.grp = c.grp, time.grp = t.grp, rep.grp = r.grp) plotProfileMB.2D.BR,stats="HotellingT2", ranking=1, type="b", xlab="Time (hour)", ylab="log2(expression)") Thanks! -Daivd [[alternative HTML version deleted]]