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Journal Club for Analysis of Complex Datasets

Sebastiani et al, Nature Genetics 37:435;2005: Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia.

Goals and Data

Pattern Recognition using Bayesian Network

Quantifying Predictive Accuracy

Difficulty in Estimating Accuracy in Small Samples

propCorrect.png library(Hmisc) P <- .8 # true probability of a correct prediction N <- round(10*(2^seq(0,13,by=.25))) p <- low <- hi <- N set.seed(3) y <- rbinom(max(N), 1, P) i <- 0 for(n in N) { i <- i+1 s <- sum(y[1:n]) p[i] <- s/n cat(n,'') lim <- binconf(s, n, method='wilson') low[i] <- lim[,'Lower'] hi[i] <- lim[,'Upper'] } #pdf('/tmp/validation.pdf') png('/tmp/propCorrect.png') plot(log2(N), p, ylim=range(c(low,hi)), axes=FALSE, type='b', xlab='Number of Patients in Validation Sample', ylab='Estimated Accuracy of Diagnostic Patterns', main='Estimated Accuracy and Its Margin of Error\nWhen True Classification Accuracy is 0.8') axis(2) w <- 10*(2^seq(0,13,by=1)) axis(1, log2(w), w) lines(log2(N), low, col=gray(.7)) lines(log2(N), hi, col=gray(.7)) abline(h=P, lty=2, col=gray(.7)) dev.off()
Topic attachments
I Attachment Action Size Date Who Comment
propCorrect.pngpng propCorrect.png manage 5.9 K 14 Apr 2006 - 16:20 FrankHarrell Accuracy of Classification Accuracy as a Function of Sample Size
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Topic revision: r2 - 17 Apr 2006, FrankHarrell
 

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