Dear An-7114,
Thanks for pointing this out....it's clearly a bug in timecourse,
which I
need to fix in the next few days. Meanwhile, a quick way to get around
this is to set the argument HotellingT2.only to FALSE
i.e.
MB.2D.test <- mb.long(M2, method = "2", times = 5, reps = size,
condition.grp = trt, rep.grp = assay, out.t = T, HotellingT2.only=F)
Yu Chuan
On Thu, 31 Aug 2006, De Bondt, An-7114 [PRDBE] wrote:
>
> Dear users,
>
> The code below is the one from the timecourse vignette (first 25
lines
> generating a dataset).
> My question is related to the out.t parameter in the mb.long()
function.
> This parameter is by default FALSE but when set to TRUE, I get the
error:
> object "modt" not found.
> Are there prerequisites for the data to be able to output the
moderated
> multivariate t-statistics?
>
> Thanks in advance for your help!
>
> Best regards,
> An
>
> library(timecourse)
> SS <- matrix(c(0.01, -8e-04, -0.003, 0.007, 0.002, -8e-04,
0.02,
> 0.002, -4e-04, -0.001, -0.003, 0.002, 0.03, -0.005,
-0.009,
> 0.007, -4e-04, -0.005, 0.02, 8e-04, 0.002, -0.001,
-0.009,
> 8e-04, 0.07), ncol = 5)
> sim.Sigma <- function() {
> S <- matrix(rep(0, 25), ncol = 5)
> x <- mvrnorm(n = 10, mu = rep(0, 5), Sigma = 10 * SS)
> for (i in 1:10) S <- S + crossprod(t(x[i, ]))
> solve(S)
> }
> sim.data2 <- function(x, indx = 1) {
> mu <- rep(runif(1, 8, x[1]), 5)
> if (indx == 1)
> res <- c(as.numeric(t(mvrnorm(n = 3, mu = mu +
rnorm(5,
> sd = 5), Sigma = sim.Sigma()))),
as.numeric(t(mvrnorm(n = 3,
> mu = mu + rnorm(5, sd = 3.2), Sigma = sim.Sigma()))))
> if (indx == 0)
> res <- as.numeric(t(mvrnorm(n = 6, mu = mu + rnorm(5,
> sd = 3), Sigma = sim.Sigma())))
> res
> }
> M2 <- matrix(rep(14, 1000 * 30), ncol = 30)
> M2[1:20, ] <- t(apply(M2[1:20, ], 1, sim.data2))
> M2[21:1000, ] <- t(apply(M2[21:1000, ], 1, sim.data2, 0))
>
> trt <- rep(c("wt", "mt"), each = 15)
> assay <- rep(rep(c("rep1", "rep2", "rep3"), each = 5), 2)
> size <- matrix(3, nrow = 1000, ncol = 2)
> MB.2D <- mb.long(M2, method = "2", times = 5, reps = size,
> condition.grp = trt,
> rep.grp = assay) # works fine
> MB.2D.test <- mb.long(M2, method = "2", times = 5, reps =
size,
> condition.grp = trt,
> rep.grp = assay, out.t = T) # generates the
following
> error
> Error in mb.2D(object, times, reps, prior.df, prior.COV,
prior.eta,
> condition.grp, :
> object "modt" not found
>
>
>
> [[alternative HTML version deleted]]
>
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