Displaying 6 results from an estimated 6 matches for "her2".
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2013 Apr 02
0
coxph and variables
...I have a set of survival data (patient who had (or died from) a
breast cancer) I'd like to see which are the variables that might cause dead
or not.When trying> summary(coxph(Surv(Time_to_distant_recurrence_yrs,
!Distant_recurrence)~ as.factor(Herceptincat) + as.factor(nodeCat_all) ,
data = her2.matrix))I obtain
Call:coxph(formula = Surv(Time_to_distant_recurrence_yrs,
!Distant_recurrence) ~ as.factor(Herceptincat) + as.factor(nodeCat_all),
data = her2.matrix) n= 231, number of events= 53
coef exp(coef) se(coef) z Pr(>|z|) as.factor(Herceptincat)1...
2011 Nov 30
0
formula for calculating the survival probability for nomogram
...alculate total points and probability *in
original data set* used for building the nomogram. *My question is how I get
the formula for calculating the survival probability for this nomogram. Then
I can use this formula to do validation by using other data set. *
f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+cytcyt+Cyt_PCDK2 ,
data=data11,
surv=T, x=T, y=T, time.inc=5)
surv<- Survival(f1)
surv10 <- function(lp) surv(10,lp)
surv5 <- function(lp) surv(5,lp)
quant <- Quantile(f1)
at.surv <- c(0.1, 0.3, 0.5, 0.7, 0.9)
nom<- nomogram(f1, conf.int=F,
fun=list(surv...
2012 May 21
1
Complex text parsing task
...l start Erbitux. ...",
" ... Ordered KRAS testing. Waiting for results. ...", " ... Patient is KRAS negative. Started Erbitux on 03/01/2011. ...",
" ... Received KRAS results on 10/20/2010. Test results indicate tumor is wild type. Ua Protein positve. ER/PR positive. HER2/neu positve. ...",
" ... Still need to order KRAS mutation testing. ... ", " ... Tumor is negative for KRAS mutation. ...",
" ... Tumor is wild type. Patient is eligible to receive Eribtux. ...",
" ... Will conduct KRAS mutation testing prior to initiation...
2011 Nov 30
1
Nomogram with stratified cph in rms package, how to get failure probability
...rms package to make a nomogram. I was able to make
a beautiful one. However, I want to change 5-year survival probability to
5-year failure probability.
I couldn?t get hazard rate from Hazard(f1) because I used cph for the model.
Here is my code:
library(rms)
f1 <- cph(Surv(retime,dfs) ~
age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11,
surv=T, x=T, y=T, time.inc=5)
surv<- Survival(f1)
haz<- Hazard(f1)
Here is the Error in UseMethod("Hazard") :
no applicable method for 'Hazard' applied to an object of class "c('cph',
'Design',...
2011 Nov 29
2
Nomogram with stratified cph in Design package-- failure probability
...l's design package to make a nomogram. I was able to
make a beautiful one. However, I want to change 5-year survival probability
to 5-year failure probability.
I couldn?t get hazard rate from Hazard(f1) because I used cph for the model.
Here is my code:
f1 <- cph(Surv(retime,dfs) ~
age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11,
surv=T, x=T, y=T, time.inc=5)
surv<- Survival(f1)
haz<- Hazard(f1)
Here is the Error in UseMethod("Hazard") :
no applicable method for 'Hazard' applied to an object of class "c('cph',
'Design'...
2012 Jan 03
0
Job opportunity in AMSTERDAM: ANALYSIS OF NGS CANCER DATA
...ing this problem from two different angles. First, we have acquired large panels of human tumors, on which we are currently performing kinase exon sequencing. More specifically, we are performing sequencing on 1) 400 samples from the NEO-ALTTO study to find alterations associated with resistance to HER2 targeted therapies; 2) at least 200 colorectal samples and 300 breast cancers (triple negatives and invasive lobular carcinomas) to detect alterations frequently occurring in these patient populations. A very strong feature of all these datasets is that matched controls are available to ensure high...