Hi, I got the error message: > out1 <- mb.long(foldM,times = 11, time.grp=times, reps = size1, rep.grp = repl, out.t=TRUE,method="1D") Error in mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, time.grp, : object 'modt1' not found We have a one-condition 11 time point experiment with 2-color custom microarrays in 6 replicates. Background-correction and normalization was performed in limma, dye-swaps were taken into account by multiplying their columns by -1. The fold change values were extracted into a matrix object foldM > dim(foldM) [1] 17328 66 > times [1] 9 9 9 9 9 9 16 16 16 16 16 16 23 23 23 23 23 23 30 30 30 30 30 30 37 [26] 37 37 37 37 37 44 44 44 44 44 44 51 51 51 51 51 51 58 58 58 58 58 58 65 65 [51] 65 65 65 65 72 72 72 72 72 72 79 79 79 79 79 79 > repl [1] "A" "B" "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" [20] "B" "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" "B" [39] "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" "B" "C" "D" "E" "F" "A" "B" "C" [58] "D" "E" "F" "A" "B" "C" "D" "E" "F" > size1<- rep(6,17328) I run timecourse on a 64-bit CentOS LINUX. I guess the problem can be in this part of mB.1D.R: 122 tol <- .Machine$double.eps 123 if(is.finite(nu) & nu > tol) 124 { 125 modS1 <- sapply(1:G, function(x) ((n[x]-1)*matrix(S1[,x],ncol=k-1)+nu*Lambda1)/(n[x]-1+nu)) 126 if(is.null(eta) & (T2.only==FALSE)) 127 { 128 sqrt.modS1 <- apply(modS1, 2, function(x) 129 svd(matrix(x,ncol=k-1))$u%*%diag(sqrt (svd(matrix(x,ncol=k-1))$d))%*%t(svd(matrix(x,ncol=k-1))$v)) 130 modt1 <- sapply(1:G, function(x) n[x]^(1/2)*solve(matrix(sqrt.modS1[,x], ncol=k-1))%*%T1%*%xbar[,x]) 131 HotellingT2 <- apply(modt1, 2, function(x) t(x)%*%x) 132 } 133 if(T2.only) 134 HotellingT2 <- sapply(1:G, function(x) 135 n[x]*t(T1%*%xbar[,x])%*%solve(matrix(modS1[,x],ncol=k-1)) %*%T1%*%xbar[,x]) 136 137 if(!is.null(eta) & (T2.only==FALSE)) 138 HotellingT2 <- sapply(1:G, function(x) 139 n[x]*t(T1%*%xbar[,x])%*%solve(matrix(modS1[,x], ncol=k-1))%*%T1%*%xbar[,x]) 140 141 } Any help would be appreciated! Thank you so much! Steve Steve Ladunga Department of Statistics University of Nebraska-Lincoln