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[#6194] Coxph interactions not working

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Date:
2015-10-14 20:09
Priority:
3
State:
Closed
Submitted by:
Lennart Karssen (lckarssen)
Assigned to:
Nobody (None)
Resolution:
Confirmation Needed
Operating System:
All
Severity:
normal
Hardware:
All
Version:
PA v0.4.5
Component:
ProbABEL
URL:
http://forum.genabel.org/viewtopic.php?f=10&t=975
 
Summary:
Coxph interactions not working

Detailed description
See also the forum post linked above.

From the forum post:

When our phenotype file includes four columns (ID, Age, Event, cov1) and the interaction parameter is specified as interaction==1, the model given is incorrect (Coxph model: ( Age , Event ) ~ mu + cov1 + SNP_A1 + mu*SNP_A1).

When the interaction parameter is specified as interaction==2, the model shown is now correct, Coxph model: ( Age , Event ) ~ mu + cov1 + SNP_A1 + cov1*SNP_A1, but the analysis doesn't run, giving the following error
error: Interaction parameter is out of range (interaction=2)

When we include a phenotype file with an additional covariate column (ID, Age, Event, cov1, cov2) and specify interaction==2, the model looks ok (with the exception of a covariate we didn't want to include), Coxph model: ( Age , Event ) ~ mu + cov1 + cov2 + SNP_A1 + cov1*SNP_A1, and the analysis seems to run, but it's not clear what analysis is being run to give the results; we can't replicate any of the results shown in R.

Followup

Message
Date: 2016-01-12 09:21
Sender: Lennart Karssen

This issue has been migrated to Github issue #15: https://github.com/GenABEL-Project/ProbABEL/issues/15

Further work and discussion on this bug will take place there.

Attached Files:

Changes:

Field Old Value Date By
close_dateNone2016-01-12 09:21lckarssen
status_idOpen2016-01-12 09:21lckarssen
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