The reason I had asked how and what method was used to calculated the confidence intervals of the odds ratio in the fisher.test is because I don't think it's the exact method based on permutations. It seems that the exact method is not implemented in R or anywhere else: "In a tactic originally suggested by Fisher, Cornfield developed an exact method for getting an odds ratio’s confidence interval. The calculations are complex and computer-intensive because iterative numerical solutions are required for quartic equations. Because of the calculational complexity, Cornfield’s method is seldom used. If you do a lot of this work, however, you might want to get and use the appropriate computer program. [The Cornfield method is not available in standard SAS, BMDP, or other packages, but can be found in the EPIINFOVersion 5 available from the Centers for Disease Control.]". Is the above correct? -- View this message in context: http://www.nabble.com/Confidence-Limits-for-a-Cross-Product-Ratio-tp24320301p24332314.html Sent from the R help mailing list archive at Nabble.com.
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