Search the entire project
This project's trackers
[#5726] ProbABEL Cox regression gives (too) many NaNs, does not match with R output
Lennart Karssen (
Lennart Karssen (lckarssen)
ProbABEL Cox regression gives (too) many NaNs, does not match with R output
The URL associated with this report points to the forum discussion. Aside from the people in the forum discussion I also got a report via e-mail about the same bug.
Comparing CoxPH regression output between R and pacoxph gives different results for many (all?) SNPs. pacoxph gives nan for those SNPs, whereas R does give output.
The reports are inconclusive about whether this behaviour is present in v0.4.3 only or also in v0.4.2.
In v0.4.2 I implemented additional convergence checks in the estimate() function of pacoxph, based on the way R checks the output.
As user wuttke points out in the forum I made a mistake there. R's survival package checks each component in the regression coefficients (beta vector) for anomalies. I misread R's code when implementing the checks. Maybe this is the cause of the problems...
Date: 2014-08-19 06:43
According to reports on the forum this bug is fixed in the coxfix branch in r1751.
Accepted As Bug