Displaying 20 results from an estimated 600 matches similar to: "Generalized Estimating Equations and a Reviewer Question I can’t answer"
2009 Sep 23
1
dotchart to barplots
Hi,
I am trying to plot the following data so that it can be visually represented well. I tried the dotchart but I felt it was too spread out. Then I tried the barplot which is good enough for me. Is there a way to give the labels for the y-axis as in the dot chart? Also, I feel the grey level is confusing, so is there options for designs within the bars? I cannot use color as the journal wants
2010 Aug 20
0
Wanted :BioInformatics Scientist - Heavy "R" focus
BioInformatics Scientist
Job Code: 10-TR25
Location: Cambridge, MA
Description
We are seeking a highly motivated, independent bioinformatics scientist
to join a group of scientists, analysts and programmers to develop tools
and methodologies for large-scale gene expression data analysis. The
group supports a variety of research projects in target and drug
discovery as well as biomarker
2012 Jul 19
2
Subsetting problem data, 2
Hello,
I didn't give enough information when I sent an query before, so I'm trying
again with a more detailed explanation:
In this data set, each patient has a different number of measured variables
(they represent tumors, so some people had 2 tumors, some had 5, etc). The
problem I have is that often in later cycles for a patient, tumors that
were originally measured are now missing (or
2011 Feb 19
0
contrasting Somer's D from Design package
Dear R help,
I am having a problem with the Design package and my problem is detailed
here.
I fit a cox model to my data and validate the Somer's Dxy using the Design
package.
(Because of computation time problem, i only try 10 bootstrap samples for
the time being)
This is the model without stratification:
> library(Design)
>
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
Hi,
The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub.
Unfortunately we don't use qsub anymore so can't test it, but it should be as follows:
R-script eg. test.R:
> ##First read in the arguments listed at the command line
> args=(commandArgs(TRUE))
>
> ##args is now a list of
2009 Jun 11
3
deSolve question
Dear All,
I like to simulate a physiologically based pharmacokinetics model using R
but am having a problem with the daspk routine.
The same problem has been implemented in Berkeley madonna and Winbugs so
that I know that it is working. However, with daspk it is not, and the
numbers are everywhere!
Please see the following and let me know if I am missing something...
Thanks a lot in advance,
2010 Aug 22
2
coxme AIC score and p-value mismatch??
Hi,
I am new to R and AIC scores but what I get from coxme seems wrong. The AIC
score increases as p-values decrease.
Since lower AIC scores mean better models and lower p-values mean stronger
effects or differences then shouldn't they change in the same direction? I
found this happens with the data set rats as well as my own data. Below is
the output for two models constructed with the rats
2009 Jan 12
1
Extraction from an output
Hello,
Would you tell my how to extract a result from a test - it's justified because I need to run this test many times. Here is an example from authors' test:
> library("coin")
> lungtumor <- data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), tumor = c(rep(c(0, 1), c(38, 2)), rep(c(0, 1), c(43, 7)), rep(c(0, 1), c(33, 15))))
> ca.test<-independence_test(tumor ~
2006 Dec 28
0
Cochran-Armitage statistics
Dear R-enthusiasts,
I am trying to do a Cochran-Armitage test for trend in R. After consulting
google I found Torsten Hothorn's remark that the 'coin' library could be
used.
lungtumor <- data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)),
tumor = c(rep(c(0, 1), c(38, 2)),
rep(c(0, 1), c(43, 7)),
2017 Jul 12
2
submitting R scripts with command_line_arguments to PBS HPC clusters
Dear all,
please could you advise me on the following : I've written a R script that
reads 3 arguments from the command line, i.e. :
" args <- commandArgs(TRUE)
TUMOR <- args[1]
GERMLINE <- args[2]
CHR <- args[3] ".
when I submit the R script to a PBS HPC scheduler, I do the following
(below), but ... I am getting an error message.
(I am not posting the error message,
2017 Jul 12
0
submitting R scripts with command_line_arguments to PBS HPC clusters
This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC
2006 Jan 18
0
Logistftest to select diagnostic genes
Hi, all,
Anyone has experience on Logistf package? I am using logistftest in Logistf
package to selelct diagnosis genes. The result seems not the same as I
expected.
I have 10 gene expression data for 27 tumor 1 and 11 tumor 0. I want to
select the best one using Maximum likelihood ratio test in logistic
regression model. This is the way my code works:
1. Read in 10 genes as independent
2007 Nov 01
1
Help me in Cochran armitage trend test Coding
Dear sir,
I am Shibu John from Thrombosis Research Institute India. It is a
multidisciplinary organisation concerned with the interrelated problems of
thrombosis and atherosclerosis.
I was searching for Cochran armitage trend test program in R. Then I had
seen your R coding for C-A trend test. I tried that in the R software.
But I can?t run the program due the [Error: could not find function
2010 Dec 16
1
defining a formula method for a weighted lm()
In the vcdExtra package on R-Forge, I have functions and generic methods
for calculating log odds ratios
for R x C x strata tables. I'd like to define methods for fitting
weighted lm()s to the resulting loddsratio objects,
but I'm having problems figuring out how to do this generally.
# install.packages("vcdExtra", repos="http://R-Forge.R-Project.org")
2007 Aug 07
1
Classifly problems
Hello,
I am trying to explore a classification with GGobi. I am trying to
generate additional data according to the model so I can draw the
decision boundaries on the GGobi plot. The problem is that I always get
the same error: Error in predict.lda(model,data): wrong number of
variables, even if I know that I used the same number of variables for
the model generation (6) and for the additional
2007 Jul 04
0
Sorting the levels of a factor
Dear Chunxu,
I'm cc'ing my reply to the r-help mailing list. As I said in one of
my previous replies to you, your questions really have to do with use
of factors in R rather than anything specifically to do with the
limma package, so they should go to a help list.
The levels() function in R, when applied to a factor, is simply an
extractor function. It extracts the levels attribute
2008 Feb 27
2
problem with creation of eSet
Hi,
I am having troubles with creating an eSet and would appreciate any help on
the following problem.
I am trying to create an eSet using the following code
pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
colnames(pd) <- c("type","tumor","time","id");
pdN <- list(type =
2007 Aug 20
1
LDA decission boundaries
Hello,
I would like to plot the results of a LDA analysis plotting the
discriminant scores with the decission boundaries on it with rggobi. I
have GGobi already installed on my computer. I have three classes, so
the plot would be LD1xLD2 plus the decission boundaries. Here there is
the code I use make the plot:
library(MASS)
data <- zgcppr273K.pca$x[,1:7]
Tumor <-
2002 Jun 24
1
Please, explicitly quote the source of non-base functions
Sirs,
No doubt many of the cerebral and erudite correspondents on the
R-list have memorized all the functions in all the CRAN
packages.
But for the benefit of those less competent, such as I, could
posters explicitly quote the source of non-base functions?
Lately, intervals() and chron() were discussed on the list,
without clear mention that they live in packages `nlme' and
2007 Jun 07
3
How to load a big txt file
Dear list,
I need to read a big txt file (around 130Mb; 23800 rows and 49 columns)
for downstream clustering analysis.
I first used "Tumor <- read.table("Tumor.txt",header = TRUE,sep = "\t")"
but it took a long time and failed. However, it had no problem if I just put
data of 3 columns.
Is there any way which can load this big file?
Thanks for any suggestions!