From: array chip <arrayprofile_at_yahoo.com>

Date: Wed, 18 May 2011 09:33:11 -0700 (PDT)

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. Received on Wed 18 May 2011 - 16:34:52 GMT

Date: Wed, 18 May 2011 09:33:11 -0700 (PDT)

> dat<-read.table("dat.txt",sep='\t',header=T,row.names=NULL)

*> d<-datadist(dat)
**> options(datadist='d')
*

> library(rms)

> (fit<-lrm(response~x,data=dat,x=T,y=T))

Logistic Regression Model

lrm(formula = response ~ x, data = dat, x = T, y = T)

Model Likelihood Discrimination Rank Discrim. Ratio Test Indexes Indexes Obs 150 LR chi2 17.11 R2 0.191 C 0.763 0 128 d.f. 1 g 1.209 Dxy 0.526 1 22 Pr(> chi2) <0.0001 gr 3.350 gamma 0.528 max |deriv| 1e-11 gp 0.129 tau-a 0.132 Brier 0.111 Coef S.E. Wald Z Pr(>|Z|) Intercept -5.0059 0.9813 -5.10 <0.0001 x 0.5647 0.1525 3.70 0.0002

As you can see, the odds ratio for x is exp(0.5647)=1.75892.

But if I run the following using summary():

> summary(fit)

Factor Low High Diff. Effect S.E. Lower 0.95 Upper 0.95 x 3.9003 6.2314 2.3311 1.32 0.36 0.62 2.01 Odds Ratio 3.9003 6.2314 2.3311 3.73 NA 1.86 7.49

What are these output? none of the numbers is the odds ratio (1.75892) that I calculated by using exp().

Can any explain?

Thanks

John

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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. Received on Wed 18 May 2011 - 16:34:52 GMT

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