[#5726] ProbABEL Cox regression gives (too) many NaNs, does not match with R output

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Date: 2014-05-26 13:43	Priority: 4
State: Closed
Submitted by: Lennart Karssen (lckarssen)	Assigned to: Lennart Karssen (lckarssen)
Resolution: Fixed	Operating System: All
Severity: major	Hardware: All
Version: PA v0.4.3	Component: ProbABEL
URL: http://forum.genabel.org/viewtopic.php?f=10&t=866
Summary: ProbABEL Cox regression gives (too) many NaNs, does not match with R output
Detailed description 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...

Followup Message Date: 2014-08-19 06:43 Sender: Lennart Karssen According to reports on the forum this bug is fixed in the coxfix branch in r1751.

Attached Files:

Changes: Field Old Value Date By Resolution Accepted As Bug 2014-10-28 08:48 lckarssen close_date None 2014-10-28 08:48 lckarssen status_id Open 2014-10-28 08:48 lckarssen