15/06/09 - ARI Meeting minutes

Meeting date : 15th June 2009 Monday 4:30pm to 6:00pm
Attended by : John, Olivier, Sam

Minutes :

1) Presentation of first nomograms

i. Nomograms using cross tabulation (number of records for each combination of the input variable) and generated using a sampling method without replacement (a record can only be selected once in each sample). A table is generated for each sample and an average nomogram is calculated at the end of the iterations (50) providing also the standard deviation.
The nomogram shows some surprising values. In some cases, the chance of the cancer to be Organ Confined is higher with a Gleason Score greater than 8 than with a Gleason Score of "4+3" or "3+4".

ii. Nomograms using binary logistic regression (closer to what have been done in Makarov's study).
The table seems to match the Partin table even if more work has to be done to reach the same level of accuracy.


2) Notes on logistic regression

Some tests such as R-Square run in SPSS (our statistic tool) shows that the logistic regression is not a method which fits well the data. This would need further study.
We also pointed out that logistic regression predicts cases that have not been recorded in the dataset and can gives high probabilities for such cases (up to 19%). This also raises the question of how well adapted to the problem the logistic regression is.


3) Nomograms to be generated next

i. Using binary logistic regression, use sampling with replacement to smoothen some high values and to get closer to what had been done by Partin.

ii. As Partin actually used a multivariate logistic regression (output can take more than two values), it would be ideal to masterize it and use it on our dataset rather than the binary regression used so far (output can take the values "1" or "0", therefore our pathological stage variable has been divided between four variables, each of them representing a stage).

iii. Partin calibrated his method using a LOESS curve. This should be also run to get a nomogram using the exact same method as Partin. This would allow us to study differences between the UK and US populations on a similar study. Expected figures should not show a huge difference according to Sam.

iv. Finally, a cross tabulation table using the figures of Partin would be interresting to see and to be compared with ours.


4) We have been successfull on the NRP funding application !


5) Next meeting : Monday 20th July 2009, 4:30pm, Ward 44 Seminar Room