[BioC] Timecourse package - mb.long() - out.t = T: object "modt" not fou nd

[Yu Chuan Tai]

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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