I am trying to use the timecourse package to analyze gene expression data in a multiseries experiment with the following design: 3 time points (6,24,48 hrs) 5 biological conditions (1 to 5) 2665 genes 2 biological replicates per condition expect for the last one that has 6 replicates. (individuals 1 to 14) In total I have 42 slides, thus the dimensionality of my data matrix is 2665x42 I create the different parameters for the mb.MANOVA function > size2 <- matrix(rep(c(2,2,2,2,6),2665), ncol=5, byrow=T) > assay2 [1] "rep1" "rep1" "rep1" "rep2" "rep2" "rep2" "rep3" "rep3" "rep3" "rep4" "rep4" "rep4" "rep5" "rep6" "rep7" "rep5" "rep6" [18] "rep7" "rep5" "rep6" "rep7" "rep8" "rep8" "rep8" "rep9" "rep9" "rep9" "rep10" "rep10" "rep10" "rep11" "rep11" "rep11" "rep12" [35] "rep13" "rep14" "rep12" "rep13" "rep14" "rep12" "rep13" "rep14" >trt2 [1] 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 5 5 5 5 5 5 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 5 5 5 5 5 5 > time2 [1] 6 24 48 6 24 48 6 24 48 6 24 48 6 6 6 24 24 24 48 48 48 6 24 48 6 24 48 6 24 48 6 24 48 6 6 6 24 24 24 48 48 When I execute the mb.MANOVA, I get the following error: > result <- mb.MANOVA(data42, times=3, D=5, size=size2, rep.grp=assay2, condition.grp=trt2, time.grp=time2) Error in squeezeVar(diagSp[x, ], N - D) : lengths differ Any idea what I am doing wrong and how to fix it?? Thanks! Ana O @@@@@ Ana Conesa, PhD. @@@ O @@ O @ Centro de Gen?mica @ O @@@@ O @ Instituto Valenciano de Investigaciones Agrarias (IVIA) @@@ O @@@@ Carretera Moncada - Naquera, Km. 4,5 @@@@ O @ 46113 Moncada (Valencia) SPAIN || Tel. +34 963424000 ext.70161; Fax. +34 963424001 || email: aconesa at ivia.es