**
I am using the following way to get p-values from fiser exact test.
However, I do need to print for each pair the values n00, n01, n10, n11.
How can I print that as a table and not a matrix as below along with the
p-value? Any help will be greatly appreciated
fish - function(y, x) {n00 =
)
}
Jean
On Mon, Jun 24, 2013 at 6:09 AM, Angel Russo angerusso1...@gmail.comwrote:
**
I am using the following way to get p-values from fiser exact test.
However, I do need to print for each pair the values n00, n01, n10, n11.
How can I print that as a table and not a matrix as below along
] - mat1$GENE SYMBOL[i]
results[count, gene2] - mat2$GENE SYMBOL[j]
results[count, 3:7] - fish(mat1[i, -1], mat2[j, -1])
}}
On Mon, Jun 24, 2013 at 10:35 AM, Angel Russo angerusso1...@gmail.comwrote:
Sample data is as follows (for simplicity assume mat1 and mat2 are the
same matrices). Also
I want to draw boxplot where the geom_points are displayed based on
ERBB2.MUT subset and they should be displayed in the right box (based
both on the ERBB2.2064 field and ERBB2_Status).
However, given my command I currently only see red points corresponding
to MUT subset in one straight line
Hello,
I have a binary matrix of 80k sets (sets comprising of combination of
cities) by 885 cities
(dimension = 80k x 885). For matrix, 1 means city is a part of the set and
0 means the city is not part of the set.
Sets are rows and cities are columns (city.test).
I want to do feature reduction
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
Thanks co much Martin for your bug reply.
I will follow up with it.
Best,
Angel
On Tue, Oct 4, 2011 at 7:35 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/04/2011 02:44 PM, Angel Russo wrote:
Hi All,
I have an CBS segmentation algorithm output for 10 tumor samples each from
2
I have two questions:
1) Can anyone provide me with a reference regarding calculation of Hazard
ratio for two groups of data. How is it being manually calculated with an
example. Unlike median time ratio which is the ratio of median times in two
groups, at what time is the hazard ratio
I need to force a coxph() function in R to use a pre-calculated set of beta
coefficients of a gene signature consisting of xx genes and the gene
expression is also provided of those xx genes.
If I try to use coxph() function in R using just the gene expression data
alone, the beta coefficients
6:08 PM, Angel Russo wrote:
I need to force a coxph() function in R to use a pre-calculated set of
beta
coefficients of a gene signature consisting of xx genes and the gene
expression is also provided of those xx genes.
I would have guessed (and that is all one can do without an example
How can I compute pairwise p-values in Kaplan-meier plots for three or more
groups?
bin.1-cut(score,c(-1000,-1,1,1000),c(low,intermediate,high))
I use km.coxph.plot currently which reports one p-value.
Thanks very much.
[[alternative HTML version deleted]]
of
e1071::SVN and ROCR here
https://heuristically.wordpress.com/2009/12/23/compare-performance-machine-learning-classifiers-r/
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Angel Russo
Sent: Monday, February 21, 2011 3:34 PM
*Hi,
*Does anyone know how can I show an *ROC curve for R-SVM*? I understand in
R-SVM we are not optimizing over SVM cost parameter. Any example ROC for
R-SVM code or guidance can be really useful.
Thanks, Angel.
[[alternative HTML version deleted]]
library(ROCR)
library(e1071)
svmres.prob - svm(traindx, traindy, probability=TRUE)
svmpred.prob - predict(svmres.prob, testdx, probability = TRUE,
decision.values = TRUE, type=prob)
print(length(attr(svmpred.prob, probabilities)))
[1] 0
print(attr(svmpred.prob, probabilities))
NULL
How can I get the list of non-zero features from svmpath at any given
lambda? All I get is following information and information about what
features were selected. In Iris example, we have 4 features and 60 cases. In
my own example which is 200cases by 300 features, I can't figure out how to
print
Greetings:
I am trying to use your R code for R-SVM as follows. Why it dosen't print
the LOO.error and the list of features?
http://www.stanford.edu/group/wonglab/RSVMpage/R-SVM.html
My training data as follows contains 142 cases and 264 features. instead I
get en error as below invalid
Hi All,
In absence of any reply, I am posting a slightly modified question. What is
x in hazard.ratio in the command below?
example(hazard.ratio)
binscores-cut(scores.train,c(-1000,-1,1,1000),c(low,intermediate,high))
*
hazard.ratio(x=?, surv.time=train$ProgFreeSurv,
HI,
I am interested in calculating hazard ratio of the stratified groups defined
by me.
library(survcomp)
binscores -
cut(scores.train,c(-1000,-1,1,1000),c(low,intermediate,high))
dd - data.frame(surv.time=OS, surv.event= status, strat=binscores)
km.coxph.plot(formula.s=Surv(surv.time,
Hello R helpers:
*My first message didn't pass trough filter so here it's again*
I would like to obtain probability of an event for one single patient as a
function of time (from survfit.coxph) object, as I want to find what is the
probability of an event say at 1 month and what is the
Hello:
I would like to obtain probability of an event for one single patient as a
function of time (from survfit.coxph) object, as I want to find what is the
probability of an event say at 1 month and what is the probability of an
event at 80 months and compare. So I tried the following but it
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