Displaying 20 results from an estimated 1400 matches similar to: "Logistftest to select diagnostic genes"
2005 Dec 22
2
Logistic regression to select genes and estimate cutoff point?
Hi, all,
I am new to R or even to statistics. Not sure if the question has a answer. But I couldn't find a straight forward answer in the help mailing list.
I need use MicroArray data to select several diagnostic genes between Normal samples and Tumor samples and use these genes to predict unknow samples.
Since the sample size is so small and data doesn't follow normal distribution, I am
2011 Oct 04
1
Assigning genes to CBS segmented output:
Hi All,
I have an CBS segmentation algorithm output for 10 tumor samples each from 2
different tumors.
Now, I am in an urgent need to assign gene (followed by all genes present)
that belong to a particular segment after I removed all the CNVs from
segment data. The format of the data is:
Sample Chromosome Start End Num_Probes Segment_Mean
Sample1A-TA 1 51598 76187 15
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
2010 Aug 20
0
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2012 May 18
1
help with creating a box plot
Hi:
I am looking for some help in making two boxplots next to each other.
I have a data like this:
N1 T1 N2 T2 N3 T3 N4 T4 ... Nn Tn
7 8.2 4 5 8 10 4 5 ..... 10 11
I want to have box plot for all Normal samples (N1,N2,N3,N4,,,,Nn)
and another box plot for all tumors (T1,T2,T3,T4,...Tn).
I have data in a numeric class.
If data is represented as N1
2005 Oct 27
2
how to predict with logistic model in package logistf ?
dear community,
I am a beginer in R , and can't predict with logistic model in package
logistf,
could anyone help me ? thanks !
the following is my command and result :
>library(logistf)
>data(sex2)
>fit<-logistf(case ~ age+oc+vic+vicl+vis+dia, data=sex2)
>predict(fit,newdata=sex2)
Error in predict(fit, newdata = sex2) : no applicable method for
"predict"
2013 Feb 27
1
Separation issue in binary response models - glm, brglm, logistf
Dear all,
I am encountering some issues with my data and need some help.
I am trying to run glm analysis with a presence/absence variable as
response variable and several explanatory variable (time, location,
presence/absence data, abundance data).
First I tried to use the glm() function, however I was having 2 warnings
concerning glm.fit () :
# 1: glm.fit: algorithm did not converge
# 2:
2011 Sep 27
1
model selection using logistf package
Hi everyone,
I'm wondering how to select the "best" model when using logistf? AIC does
not work neither does anova. I tried fitting a glm model but got the
separation warning message so I tried using the logistf package but as I
stepwise simplify the model I don't know if the simplification is motivated
or not... Can anyone explain to me how I should approach this problem? I
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
2008 Sep 16
1
logistf error message
I am new to using R. Currently, I am using the logistf package to run logistic regression analysis. When I run the following line of code:
attach(snpriskdata)
logisticpaper<-logistf(sascasecon~saspackyrs+newsbmi+EDUCATION+sasagedx+sasflung+condobst+sasadultasprev)
I get the following error message:
Error in sum(y) : invalid 'type' (character) of argument
What does this error
2008 Jun 07
1
error message with dat
Hello everyone,
I have two problems which I am unable to solve :
1.I am trying to add the row labels (g1-g2000) to the very left of a data table. The data
table is 2000 rows by 62 columns.I have used the following code.
read.table(file="C:\\Documents and Settings\\Owner\\My Documents\\colon cancer1.txt",header=T,row.names=1)
rowname(dat) <- paste("g", c(1:nrow(dat)),
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
2008 Mar 05
2
t.test & p-Value
Hello list,
I am trying to apply the paired t.test between diseased and not diseased
patients to identify genes that are more expressed in the one situation
under the other. In order to retrieve the genes that are more expressed in
the positive disease state I do:
p.values<-c()
for(i in 1:length(Significant[,1])){
p.values[i]<-try(t.test(positive[i,],negative[i,],alternative
2012 Jan 03
0
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2008 Jan 31
3
Memory problem?
Hello R users,
I am trying to run a cox model for the prediction of relapse of 80 cancer
tumors, taking into account the expression of 17000 genes. The data are
large and I retrieve an error:
"Cannot allocate vector of 2.4 Mb". I increase the memory.limit to 4000
(which is the largest supported by my computer) but I still retrieve the
error because of other big variables that I have in
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)),
2010 Mar 09
1
penalized maximum likelihood estimation and logistf
Hi, I got two questions and would really appreciate any help from here.
First, is the penalized maximum likelihood estimation(Firth Type Estimation)
only fit for binary response (0,1 or TRUE, FALSE)? Can it be applied to
multinomial logistic regression?
If yes, what's the formula for LL and U(beta_i)? Can someone point me to
the right reference?
Second, when I used *logistf *on a dataset with