[R] Generative Topographic Map
mauede at alice.it
mauede at alice.it
Wed Mar 31 11:09:43 CEST 2010
I tried to use R version of package
I noticed the original MatLab Pckage is much better documented.
I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created:
I wrote my own few lines as follows:
inDir <- "C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA"
setwd(inDir)
T <- read.table("DHA_TNH.txt")
L <- 3
X <- matrix(nrow=nrow(T),ncol=3,byrow=TRUE)
MU <- matrix(nrow=round(nrow(T)/5), ncol=L)
for(i in 1:ncol(X)) {
for(j in 1:nrow(X)) {
X[j,i] <- RANDU()
}
}
for(i in 1:ncol(MU)) {
for(j in 1:nrow(MU)) {
MU[j,i] <- RANDU()
}
}
sigma <-1
FI <- gtm_gbf(MU,sigma,X)
W <- gtm_ri(T,FI)
Y= FI%*%W
b = gtm_bi(Y)
lambda <- 0.001
for (m in 1:15) {
trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 0.01)
W = trnResult$W
b = trnResult$beta
Y = FI %*% W
}
I ran the above script on my own data representing 1969 samples of 7 dihedral angles of a folding molecule (attached.
Upon running the 1st iteration of the training function "gtm_trn" I get the following error that I cannot interpret.
Any help and/or suggestion is welcome:
> trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 1.)
Error in gtmGlobalR %*% T :
requires numeric/complex matrix/vector arguments
In addition: Warning messages:
1: In chol.default(A, pivot = TRUE) : matrix not positive definite
2: In gtm_trn(T, FI, W, lambda, 1, b, 2, quiet = TRUE, minSing = 1) :
Using 7 out of 395 eigenvalues
Thank you in advance,
Maura
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