Displaying 20 results from an estimated 1000 matches similar to: "How to use Cox PH model to select genes from DNA gene expression profiles?"
2003 Feb 24
2
"trace" argument in legend() (PR#2578)
Full_Name: Jerome Asselin
Version: 1.6.2
OS: RedHat Linux 7.2
Submission from: (NULL) (142.103.173.179)
Should be an easy fix...
Consider the examble below:
plot(0,0)
legend(0,0,c("Hello!","Hi!"),pch=1:2,lty=1:2,trace=T)
It gives the following trace:
> plot(0,0)
> legend(0,0,c("Hello!","Hi!"),pch=1:2,lty=1:2,trace=T)
xchar= 0.05178 ;
2003 Feb 15
2
(no subject)
Hi,
Are there some packages which can generate multi-normal, multi-t, etc
multivariate sampling? thanks!
Best wishes,
Peng
*******************************
Peng Zhang
Department of Biostatistics
Harvard School of Public Health
655 Huntington Avenue
Boston, Massachusetts 02115
*******************************
I believe I can fly
I believe I can touch the sky
2003 Feb 27
2
epoch time conversion in R
I have a data file where each entry is indexed by the time in seconds since
epoch (e.g. 1046315697). Is there an easy way to convert this time value into
a more friendly time (such as Month-Year) when plotting it?
I searched through the manual, mailing lists, and functions like as.POSIXct
and strptime, but didn't find what I need.
Thanks,
Sharad.
2003 Apr 17
1
bit set or bit test
Hello, does R have functions for setting and testing
bit values?
I want to conserve memory for storing presence/absence
data for large multiple arrays within a single array,
using element values like
present[x,y] <- ntharray[x,y]*(2^n)
where presence is 1, non-presence is 0 and n is the
nth array
e.g. 1*(2^0) + 0*(2^1) + 0*(2^2) + 1*(2^3) + 0(2^4)
for storing the value 9 for presence in
2003 Feb 24
2
fill prob. in legend
Hi,
I'm trying to construct a legend which has four lines of text and associated
symbols. The first two symbols need to be normal lines which vary only in
colour. The second two symbols should have filled boxes. How do I suppress
the fill boxes in the first two lines?
J.
2003 Apr 14
7
functions in a package
Hello,
I have a beginner's Q:
if i want to know all the functions provided by a package,
what is command for that?
in another word,
Is there a command to list all the commands available in a packege?
thanks a lot,
yan
2003 May 16
2
Efficient subsetting
Hi, I'm facing this problem quite a lot, so it seems worthwhile
to check to see what the most efficient solution is.
I've two vectors x (values ordered) and y. I've ranges
x < x0, x0 <= x < x1, x1 <= x < x2, x2 <= x < x3, x > xn
and want to construct a subvector yprime of y which consists
of the first/last value of y whose x values are in the range.
For
2003 Mar 10
1
help--Cox ph model
Dear r-users,
I want to use the Cox's ph model to analyze survival data set. How can I
extract the model coefs. and Wald test p-value or Score?
For example: I use the data set melanom in iSwR package.
> library(survival)
> data(melanom)
> attach(melanom)
> cox.model <- coxph(Surv(days,status==1)~sex)
> summary(cox.model)
Call:
coxph(formula = Surv(days, status == 1) ~
2003 Aug 07
2
segmentation fault: formula() with long variable names (PR#3680)
R version: 1.7.1
OS: Red Hat Linux 7.2
In this example, I would expect an error for the overly long variable
name. This is always reproducable for me.
> formula(paste("y~",paste(rep("x",50000),collapse="")))
Segmentation fault
Sincerely,
Jerome Asselin
--
Jerome Asselin (Jérôme), Statistical Analyst
British Columbia Centre for Excellence in HIV/AIDS
St.
2003 Aug 08
1
covmat argument in princomp() (PR#3682)
R version: 1.7.1
OS: Red Hat Linux 7.2
When "covmat" is supplied in princomp(), the output value "center" is all
NA's, even though the input matrix was indeed centered. I haven't read
anything about this in the help file for princomp(). See code below for an
example: pc2$center is all NA's.
Jerome Asselin
x <- rnorm(6)
y <- rnorm(6)
X <- cbind(x,y)
2003 Aug 30
3
fisher.test() gives wrong confidence interval (PR#4019)
The problem occurs when the sample odds ratio is Inf, such as in the
following example. Given the fact that both upper bounds of the two 95%
confidence intervals are Inf, I would have expected that the two lower
bounds be equal, but they aren't.
x <- matrix(c(9,4,0,2),2,2)
x
# [,1] [,2]
#[1,] 9 0
#[2,] 4 2
rbind("two.sided.95CI"=fisher.test(x)$conf.int,
2003 May 20
1
legend() with option adj=1
Hi there,
I want to justify to right the text of my legend. Consider this short
reproducable example.
x <- 1:5
y1 <- 1/x
y2 <- 2/x
plot(rep(x,2),c(y1,y2),type="n",xlab="x",ylab="y")
lines(x,y1)
lines(x,y2,lty=2)
legend(5,2,c("1,000","1,000,000"),lty=1:2,xjust=1,yjust=1)
2003 Feb 27
2
interval-censored data in survreg()
I am trying to fit a lognormal distribution on interval-censored
data. Some of my intervals have a lower bound of zero.
Unfortunately, it seems like survreg() cannot deal with lower
bounds of zero, despite the fact that plnorm(0)==0 and
pnorm(-Inf)==0 are well defined. Below is a short example to
reproduce the problem.
Does anyone know why survreg() must behave that way?
Is there an alternate
2003 Aug 07
2
model.frame() call from inside a function (PR#3671)
R version: 1.7.1
OS: Red Hat Linux 7.2
Hi all,
The formula object in model.frame() is not retrieved properly when
model.frame() is called from within a function and the "subset" argument
is supplied.
foo <- function(formula,data,subset=NULL)
{
cat("\n*****Does formula[-3] == ~y ?**** TRUE *****\n")
print(formula[-3] == ~y)
cat("\n*****Result of model.frame()
2003 May 21
1
axis() default values for "lty", "lwd", and "col"
Hi,
I would like to recommend a minor modification in axis() which I believe
can simplify the making of plots for publications. I am trying to define
default values for par() in order to make labels bigger and lines thicker,
so that the resulting plots look good when resized for publication
purposes. I ran into the following problem...
axis() does not use par() values as default for
2003 May 01
2
What' wrong?
I try to do single proportion test on my category data. Here is my R
script:
library("ctest")
catSignifTest <- function( catFile ) {
###############################################################
## Get the data sets from text file
catData <- read.table( catFile )
ncols <- length(catData)
nrows <- length(catData[,1])
ncol1 <- ncols - 1
probeNbr
2003 May 07
0
frailty models in survreg() -- survival package (PR#2933)
I am confused on how the log-likelihood is calculated in a parametric
survival problem with frailty. I see a contradiction in the frailty() help
file vs. the source code of frailty.gamma(), frailty.gaussian() and
frailty.t().
The function frailty.gaussian() appears to calculate the penalty as the
negative log-density of independent Gaussian variables, as one would
expect:
>
2003 Jul 04
0
degrees of freedom in nlme() (PR#2384)
I would like to document my findings (with a potential FIX) regarding the
issue of calculation of the degrees of freedom with nlme().
The program given at the bottom of this email generates and fit 20 data
sets with a mixed-effects LINEAR model, but using the function nlme()
instead of lme(). In each case, the correct number of degrees of freedom
for the intercept parameter is 12. However, in
2003 May 13
1
How to retrieve data frame column names?
Dear R-users/helpers,
Does anyone tell me how to retrieve the data frame column names?
I'm working on coxph model to analyze survival data of Affy DNA chips.
I get the coxph coef p-value for each probe and want output the probe name
with the p-value. The probe names are the data frame column names.
How can I do this?
Thanks for your help.
Guangchun
2003 Jul 15
2
"na.action" parameter in princomp() (PR#3481)
Full_Name: Jerome Asselin
Version: 1.7.1
OS: Red Hat Linux 7.2
Submission from: (NULL) (24.77.125.119)
Setting the parameter na.action=na.omit should remove
incomplete records in princomp. However this does not
seem to work as expected. See example below.
Sincerely,
Jerome Asselin
data(USArrests)
princomp(USArrests, cor = TRUE) #THIS WORKS
USArrests[1,3] <- NA
princomp(USArrests, cor =