R help - Jun 2013 - Problems in Constructing Two way Matrix

Hello,

Where is the problem in this programming. I want two way matrix, but it gives
problem.
The program is given below:

Thanks in advance.

Regards
Fazli Raziq


rep = 2
genes = 5
pred = c()
iter   = array (dim = c(rep, pred))
pred = array(dim = c(1, genes))
m = c()
l = 1
w = 1
for(m in 1:rep) {
t = time
c = cens
tab = cbind(t, c)

# Resampling Time and Censoring
cc = sample(c, replace = TRUE)
tt = sample(t, replace = TRUE)
xx = Surv(tt, cc)

P = predic[,1:5]
n = 310
ma = matrix(P, n)
boot <- sample(seq(n), replace=TRUE)
genes5 = ma[boot, ]


for(p in 1: genes){
i = c()

for(i in w:l) {
z = genes5[,w: l]
y = coxph(xx ~ z)

}
Pval = summary(y) $ coeff[, 5]

if( any(Pval <= 0.01) ) sign <- 1 else sign <- 0
pred[1, p] = sign[1]
}

iter [m, 1:5] = pred[1: 5]

}
	[[alternative HTML version deleted]]

On 19-06-2013, at 09:30, Fazli Raziq <raziq_fazli at yahoo.com> wrote:
> Hello,
> 
> Where is the problem in this programming. I want two way matrix, but it
gives problem.
What is the problem?
What are you expecting and what are you getting?
> The program is given below:
> 
> Thanks in advance.
> 
> Regards
> Fazli Raziq
> 
> 
> rep = 2
> genes = 5
> pred = c()
> iter   = array (dim = c(rep, pred))
> pred = array(dim = c(1, genes))
> m = c()
> l = 1
> w = 1
> for(m in 1:rep) {
> t = time
> c = cens
> tab = cbind(t, c)
> 
> # Resampling Time and Censoring
> cc = sample(c, replace = TRUE)
> tt = sample(t, replace = TRUE)
> xx = Surv(tt, cc)
> 
> P = predic[,1:5]
> n = 310
> ma = matrix(P, n)
> boot <- sample(seq(n), replace=TRUE)
> genes5 = ma[boot, ]
> 
> 
> for(p in 1: genes){
> i = c()
> 
> for(i in w:l) {
> z = genes5[,w: l]
> y = coxph(xx ~ z)
> 
> }
> Pval = summary(y) $ coeff[, 5]
> 
> if( any(Pval <= 0.01) ) sign <- 1 else sign <- 0
> pred[1, p] = sign[1]
> }
> 
> iter [m, 1:5] = pred[1: 5]
> 
> }
Running this code gives an error message:

Error: object 'cens' not found


And what is the purpose of t = time? time is a stats
function.
> 	[[alternative HTML version deleted]]
> 
You are asked to NOT post in html.

Berend
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

I'm cc'ing this to the R-help list.

Please reply to the list and privately.
You will get more response that way.

Your reply does not address the issue I mentioned.

Berend

On 19-06-2013, at 10:29, Fazli Raziq <raziq_fazli at yahoo.com> wrote:
> Dear Mr. Berend,
> 
> I want to construct "Two way Matrix". The Algorithm is like:
> 
> 1)  Data of time with censoring or events
> 2)  Predictor variables (genes)
> 3)  Resample data in step 1 and 2 by WR
> 4)  Apply Coxph Model to resample data. Apply Surv function to each
Predictor variable, individually.
> 5)  Give value 1 if it's P-value is less than 0.05, otherwise 0. Save
it in the first Column (Column of 0's and 1's) of the Matrix.
> 6)  Iterate the process 1 to 5, 10 times. And make 10 Columns of 0's
and 1's.
> 
> I have done the programming for it, but gives problem in Matrix.
> Thanks for replying to my mail. Hope for the best.
> 
> Best Regards
> Fazli Raziq
> 
> From: Berend Hasselman <bhh at xs4all.nl>
> To: Fazli Raziq <raziq_fazli at yahoo.com> 
> Cc: "r-help at r-project.org" <r-help at r-project.org> 
> Sent: Wednesday, 19 June 2013, 9:43
> Subject: Re: [R] Problems in Constructing Two way Matrix
> 
> 
> On 19-06-2013, at 09:30, Fazli Raziq <raziq_fazli at yahoo.com>
wrote:
> 
> > Hello,
> > 
> > Where is the problem in this programming. I want two way matrix, but
it gives problem.
> 
> What is the problem?
> What are you expecting and what are you getting?
> 
> > The program is given below:
> > 
> > Thanks in advance.
> > 
> > Regards
> > Fazli Raziq
> > 
> > 
> > rep = 2
> > genes = 5
> > pred = c()
> > iter  = array (dim = c(rep, pred))
> > pred = array(dim = c(1, genes))
> > m = c()
> > l = 1
> > w = 1
> > for(m in 1:rep) {
> > t = time
> > c = cens
> > tab = cbind(t, c)
> > 
> > # Resampling Time and Censoring
> > cc = sample(c, replace = TRUE)
> > tt = sample(t, replace = TRUE)
> > xx = Surv(tt, cc)
> > 
> > P = predic[,1:5]
> > n = 310
> > ma = matrix(P, n)
> > boot <- sample(seq(n), replace=TRUE)
> > genes5 = ma[boot, ]
> > 
> > 
> > for(p in 1: genes){
> > i = c()
> > 
> > for(i in w:l) {
> > z = genes5[,w: l]
> > y = coxph(xx ~ z)
> > 
> > }
> > Pval = summary(y) $ coeff[, 5]
> > 
> > if( any(Pval <= 0.01) ) sign <- 1 else sign <- 0
> > pred[1, p] = sign[1]
> > }
> > 
> > iter [m, 1:5] = pred[1: 5]
> > 
> > }
> 
> Running this code gives an error message:
> 
> Error: object 'cens' not found
> 
> 
> And what is the purpose of t = time? time is a stats function.
> >     [[alternative HTML version deleted]]
> > 
> 
> You are asked to NOT post in html.
> 
> Berend
> 
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
>