Dear all,
I have a question concerning the p-value. When running coxph I get a p-value
= 0. :confused:
Can this be true? Why aren?t there decimal points? Is there a way to find
out the exact p-value?
Here is the output:
----------------------------------------------------------------------------------------------------
Call:
coxph(formula = Surv(start, stop, status) ~ Albumin_gproL, data = dial,
na.action = na.omit, method = "breslow")
n=22449 (31 observations deleted due to missingness)
coef exp(coef) se(coef) z p
Albumin_gproL -0.157 0.855 0.0172 -9.16 0
exp(coef) exp(-coef) lower .95 upper .95
Albumin_gproL 0.855 1.17 0.826 0.884
Rsquare= 0.003 (max possible= 0.033 )
Likelihood ratio test = 73.6 on 1 df, p=0
Wald test = 83.8 on 1 df, p=0
Score (logrank) test = 86.1 on 1 df, p=0
> cox.zph(cox_1111)
rho chisq p
Albumin_gproL -0.0509 0.197 0.657
----------------------------------------------------------------------------------------------------
Thank you in advance...
GSt
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Because your test statistics (z=-9.16) is too small. (well, z> 1.96 or Z < -1.96 is p=0.05) If you really want the exact p, you can try pnorm(-9.16) if I were you I will quote p<0.001 as well as the test statistics. (if you are going to submit it to medical journals) C On Thu, Oct 30, 2008 at 10:36 PM, GSt <gisela.sturm at i-med.ac.at> wrote:> > Dear all, > > I have a question concerning the p-value. When running coxph I get a p-value > = 0. :confused: > Can this be true? Why aren?t there decimal points? Is there a way to find > out the exact p-value? > > Here is the output: > ---------------------------------------------------------------------------------------------------- > Call: > coxph(formula = Surv(start, stop, status) ~ Albumin_gproL, data = dial, > na.action = na.omit, method = "breslow") > > n=22449 (31 observations deleted due to missingness) > coef exp(coef) se(coef) z p > Albumin_gproL -0.157 0.855 0.0172 -9.16 0 > > exp(coef) exp(-coef) lower .95 upper .95 > Albumin_gproL 0.855 1.17 0.826 0.884 > > Rsquare= 0.003 (max possible= 0.033 ) > Likelihood ratio test = 73.6 on 1 df, p=0 > Wald test = 83.8 on 1 df, p=0 > Score (logrank) test = 86.1 on 1 df, p=0 > >> cox.zph(cox_1111) > rho chisq p > Albumin_gproL -0.0509 0.197 0.657 > ---------------------------------------------------------------------------------------------------- > > Thank you in advance... > GSt > -- > View this message in context: http://www.nabble.com/p-value%3D0-running-coxph-tp20248274p20248274.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- CH Chan Research Assistant - KWH http://www.macgrass.com
On Thu, 30 Oct 2008, GSt wrote:> Dear all,>I have a question concerning the p-value. When running coxph I get a p-value >= 0. :confused: >Can this be true? Why aren??t there decimal points? Is there a way to >find out the exact p-value?The p-values are rounded, and of course they are not exactly zero, just <0.0005. You are given the z-statistic so you could compute the p-value> 2*pnorm(-9.16)[1] 5.189732e-20 Now, this number is probably pretty useless because the Normal approximation to the test statistic doesn't work that far out in the tails unless you have a very large number of events. It's also unusual for the null hypothesis to be even slightly interesting when the p-value is that small -- do you really not know whether albumin concentrations are related to the outcome? -thoams Here is the output: ---------------------------------------------------------------------------------------------------- Call: coxph(formula = Surv(start, stop, status) ~ Albumin_gproL, data = dial, na.action = na.omit, method = "breslow") n=22449 (31 observations deleted due to missingness) coef exp(coef) se(coef) z p Albumin_gproL -0.157 0.855 0.0172 -9.16 0 exp(coef) exp(-coef) lower .95 upper .95 Albumin_gproL 0.855 1.17 0.826 0.884 Rsquare= 0.003 (max possible= 0.033 ) Likelihood ratio test = 73.6 on 1 df, p=0 Wald test = 83.8 on 1 df, p=0 Score (logrank) test = 86.1 on 1 df, p=0> cox.zph(cox_1111)rho chisq p Albumin_gproL -0.0509 0.197 0.657 ---------------------------------------------------------------------------------------------------- Thank you in advance... GSt -- View this message in context: http://www.nabble.com/p-value%3D0-running-coxph-tp20248274p20248274.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle