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[#1266] pacoxph with no covariates

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Date:
2011-02-03 13:04
Priority:
3
State:
Closed
Submitted by:
Yurii Aulchenko (yurii)
Assigned to:
Lennart Karssen (lckarssen)
Resolution:
Fixed
Operating System:
All
Severity:
minor
Hardware:
All
Version:
None
Component:
ProbABEL
URL:
 
Summary:
pacoxph with no covariates

Detailed description
From Aron Joon:

We tried to run Cox models using pacoxph

An error message will come up as "nc <=0" when I tried to model "phenotype : SNPs" (ie, no covariate). Is there a trick how to fix this? I added a constant dummy (covariate) variable (all values = 1) in order to get ProbABEL run smoothly

Followup

Message
Date: 2015-03-17 13:55
Sender: Lennart Karssen

Fixed in r1931.
Date: 2015-03-06 10:50
Sender: Lennart Karssen

See also Bug #6041 for more (possibly related?) info.
Date: 2015-01-25 17:32
Sender: Lennart Karssen

According to one user report sent to me by e-mail, as of ProbABEL v0.4.4, the dummy covariate work-around doesn't work any more, but leads to the error message "X matrix deemed to be singular, setting beta and se to 'NaN'" for all SNPs.

With a non-constant covariate (e.g. sex), the output is ok.
Date: 2014-05-26 14:59
Sender: Lennart Karssen

I added a check for this bug in r1740.
Currently the check is listed as XFAIL (expected FAIL) in Makefile.am. Once this bug is fixed, 'make check' should give an error (and the check should be listed as XPASS). That's the time to remove the XFAIL line from Makefile.am and to extend the check to include a diff with verified data.
Date: 2014-03-16 12:01
Sender: Lennart Karssen

Correction to the previous message, the SVN revision number was r1644 (this is the revision in which I slightly edited the error message).
Date: 2014-03-16 11:58
Sender: Lennart Karssen

I just ran into this bug (PA SVN r1631).
The "nc <- 0" message appears when ProbABEL is not compiled with EIGEN. If EIGEN is used, then the message is:
mematrix(): number of columns less than 1

Attached Files:

Changes:

Field Old Value Date By
assigned_tonone2015-03-17 13:56lckarssen
HardwareNone2015-03-17 13:55lckarssen
Operating SystemNone2015-03-17 13:55lckarssen
ResolutionAccepted As Bug2015-03-17 13:55lckarssen
close_dateNone2015-03-17 13:55lckarssen
status_idOpen2015-03-17 13:55lckarssen
priority12015-01-25 17:32lckarssen
Thanks to:
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