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
**
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 = s
pval = fisher.test(a)$p.value
> return(pval)
> }
>
> Jean
>
>
> On Mon, Jun 24, 2013 at 6:09 AM, Angel Russo wrote:
>
>> **
>>
>> I am using the following way to get p-values from fiser exact test.
>> However, I do need to print for each pair the values
1 0 0 0 0 0 0 0 0 0 0 0 0 0 ADRBK2 0 0 0 0
>> 0 1 0 0 0 0 0 0 0 AKT1 0 0 0 0 0 0 0 0 0 0 0 0 0 AKT2 0 0 0 0 0 0 0 0 0
>> 0 0 1 0 AKT3 0 0 0 0 0 0 0 0 1 0 0 1 0 ALK 0 0 0 0 0 0 0 0 0 0 0 0 0
>>
>>
>> On Mon, Jun 24, 2013 at 11:03 AM, Adams, Jean wrote:
>>
>
Hello R helpers:
*My first message didn't pass trough filter so here it's again*
I would like to obtain probability of an event for one single patient as a
function of time (from survfit.coxph) object, as I want to find what is the
probability of an event say at 1 month and what is the probabilit
Hello:
I would like to obtain probability of an event for one single patient as a
function of time (from survfit.coxph) object, as I want to find what is the
probability of an event say at 1 month and what is the probability of an
event at 80 months and compare. So I tried the following but it fai
HI,
I am interested in calculating hazard ratio of the stratified groups defined
by me.
library(survcomp)
binscores <-
cut(scores.train,c(-1000,-1,1,1000),c("low","intermediate","high"))
dd <- data.frame("surv.time"=OS, "surv.event"= status, "strat"=binscores)
km.coxph.plot(formula.s=Surv(surv.t
Hi All,
In absence of any reply, I am posting a slightly modified question. What is
"x" in hazard.ratio in the command below?
example(hazard.ratio)
binscores<-cut(scores.train,c(-1000,-1,1,1000),c("low","intermediate","high"))
*
hazard.ratio(x=?, surv.time=train$ProgFreeSurv,
surv.event=train$
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 'digits
*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.
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_
> 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
drew Ziem wrote:
> In addition's to Max's suggestion about caret, look at ROCR which
> visualizes ROC charts for any binary classifier. I have an example of
> e1071::SVN and ROCR here
>
>
> https://heuristically.wordpress.com/2009/12/23/compare-performance-machine
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 a
c(0.05, -0.05), iter.max = 0)
>>
>
>
>>
>> I hope it helps.
>>
>> Best,
>> Dimitris
>>
>>
>> On 3/13/2011 6:08 PM, Angel Russo wrote:
>>
>>> I need to force a coxph() function in R to use a pre-calculated set of
>>> beta
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.
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___
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 calculation
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 wrote:
> On 10/04/2011 02:44 PM, Angel Russo wrote:
>
>> Hi All,
>>
>> I have an CBS segmentation algorithm output for 10 tumor samples eac
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