>From the timecourse vignete: "For version 1.0.0, missing time point samples are not allowed inmb.long() andmb.MANOVA(), while missing replicates are allowed for a subset of genes." Is this missing data only allowed for a subset of genes or for a whole replicate? We have a data set with 5 times points: time0 - animal 1, animal 2, and animal 3 time1 - animal 4, animal 5, and animal 6 time2 - animal 7, and animal 8 time3 - animal 9, animal 10, animal 11 time4 - animal 12, animal 13, animal 14 So, time 2 has only 2 replicates. I try this code: > assay <- c("d1", "d1", "d1", "d1", "d2", "d2", "d2", "d2", "d2", "d3", "d3", "d3", "d3", "d3") > time.grp <- c(1, 2, 4, 5, 1, 2, 3, 4, 5, 1, 2, 3, 4, 5) > time.grp > dim(todos.timecourse.matrix) [1] 9600 14 > size <- read.table("reps.csv", sep="\t", header=TRUE) > size.matrix = size[,2:6] > row.names(size.matrix) = size[,1] > size.matrix[1:10,] T0 T1 T2 T3 T4 gene1 3 3 2 3 3 gene2 3 3 2 3 3 gene3 3 3 2 3 3 gene4 3 3 2 3 3 gene5 3 3 2 3 3 gene6 3 3 2 3 3 gene7 3 3 2 3 3 gene8 3 3 2 3 3 gene9 3 3 2 3 3 gene10 3 3 2 3 3 > > out1 <- mb.long(todos.timecourse.matrix, times = 5, reps = size.matrix, + rep.grp = assay, time.grp = time.grp, HotellingT2.only = FALSE) Error in mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, time.grp, : The sample sizes are incorrect. > Are there a way to analysis this data on timecourse package? Am I doing any mistake or misinterpretation? Thank you very much -- Marcelo Luiz de Laia Brazil Linux user number 487797

Hi Marcelo, The current version of Timecourse is for longitudinal time course data only. Based on what you described below, your study looked like a cross-sectional one because time point samples were from different animals. That's, they were independent. I'd suggest that you use other software for analyzing your data, e.g. limma. The cross-sectional method will be built in timecourse in the future. Best, Yu Chuan On Mon, 8 Feb 2010, Marcelo Laia wrote: >> From the timecourse vignete: > > "For version 1.0.0, missing time point samples are not allowed > inmb.long() andmb.MANOVA(), > while missing replicates are allowed for a subset of genes." > > Is this missing data only allowed for a subset of genes or for a whole > replicate? > > We have a data set with 5 times points: > > time0 - animal 1, animal 2, and animal 3 > time1 - animal 4, animal 5, and animal 6 > time2 - animal 7, and animal 8 > time3 - animal 9, animal 10, animal 11 > time4 - animal 12, animal 13, animal 14 > > So, time 2 has only 2 replicates. > > I try this code: > >> assay <- c("d1", "d1", "d1", "d1", "d2", "d2", "d2", "d2", "d2", > "d3", "d3", "d3", "d3", "d3") > >> time.grp <- c(1, 2, 4, 5, 1, 2, 3, 4, 5, 1, 2, 3, 4, 5) >> time.grp > >> dim(todos.timecourse.matrix) > [1] 9600 14 > >> size <- read.table("reps.csv", sep="\t", header=TRUE) >> size.matrix = size[,2:6] >> row.names(size.matrix) = size[,1] > >> size.matrix[1:10,] > T0 T1 T2 T3 T4 > gene1 3 3 2 3 3 > gene2 3 3 2 3 3 > gene3 3 3 2 3 3 > gene4 3 3 2 3 3 > gene5 3 3 2 3 3 > gene6 3 3 2 3 3 > gene7 3 3 2 3 3 > gene8 3 3 2 3 3 > gene9 3 3 2 3 3 > gene10 3 3 2 3 3 >> > >> out1 <- mb.long(todos.timecourse.matrix, times = 5, reps = size.matrix, > + rep.grp = assay, time.grp = time.grp, > HotellingT2.only = FALSE) > Error in mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, > time.grp, : > The sample sizes are incorrect. >> > > > Are there a way to analysis this data on timecourse package? > > Am I doing any mistake or misinterpretation? > > Thank you very much > > -- > Marcelo Luiz de Laia > Brazil > Linux user number 487797 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >