> On Jul 24, 2016, at 8:20 AM, Qinghua He via R-help <r-help@r-project.org>
> wrote:
>
> Dear all,
> I have the following table for a breast cancer study and I was trying to
> calculate the odds ratio of different subtypes based on AR (AR+ as the base
> case).
> AR- AR+Luminal A 1 19Luminal B 1 15Her2
> 0 4Basal-like 20 1Normal Like 2 2
> I did Firth logistic regression using the model:
> fit <- logistf(AR ~
> Age+LumA+LumB+HER2+Basal+Normal-1,data=df).summary(fit)exp(coef(fit))exp(confint(fit))
Edited from the HTML-garbled posting that appeared. Rhelp is a plain text
mailing list and HTML ends up as a mess.
coef se(coef) lower 0.95 upper 0.95 Chisq p
Age 0.02675758 0.03138425 -0.03462915 0.09404934 0.7210455 0.39580118
LumA -4.04312870 2.08208148 -8.91195072 -0.32580912 4.6216454 0.03157094
LumB -3.74769116 1.96613514 -8.19454796 -0.16290619 4.2262682 0.03980286
HER2 -3.71796180 2.45080140 -9.50654675 0.54467296 2.8798910 0.08969209
Basal 1.12126338 1.83884710 -2.45335167 5.00553060 0.3763601 0.53955773
Normal -1.51899257 2.05597939 -5.97976670 2.40100862 0.5806537 0.44605621
> My question is: how come the p-value of Basal is so large? I was expecting a
> smaller p-value than LumA or LumB.
Your question is not on-topic for Rhelp., since it really has nothing to do
with problems in R programming. You should be posing the question on a mailing
list or a web forum where purely statistical questions are welcomed. I would
expect that you would get a followup question asking you for more information,
since there are many aspects of datasets that may affect p-values that you have
not yet described. You for instance have not even described what "AR" might be.
I'd suggest that you first read the Posting Guide and then post a question on
http://stats.stackexchange.com with some more information about the study and
better descriptive statistics about your population size and the covariates.
> Some extra information:
>> exp(coef(fit))
>> Age LumA LumB HER2 Basal Normal
>> 1.02711878 0.01754250 0.02357211 0.02428341 3.06872873 0.21893233
>> exp(confint(fit))
>> Lower 95% Upper 95%
>> Age 9.659636e-01 1.0986139
>> LumA 1.347687e-04 0.7219430
>> LumB 2.761551e-04 0.8496709
>> HER2 7.436339e-05 1.7240445
>> Basal 8.600484e-02 149.2362476
>> Normal 2.529416e-03 11.0343002
> If I calculate odds ratio using an online calculator based on: AR-
> AR+Basal 20 1Non-basal 4 40
> I got:
> OR:200 95% CI: 20.9510 to 1909.2138 p < 0.0001
> Can someone please help me explain?
> Thank you very much!
> Peter
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
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