[BioC] timecourse package - Missing data

[Marcelo Laia]

>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