[GenABEL-dev] [ProbABEL] Different results when using fv and regular input on 64 bit Linux

[L.C. Karssen]

Dear list,

Over the weekend I spent some more time looking into this problem. I've
opened bug #1889 for it:
https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=1889&group_id=505

It turns out to be a problem with passing the inverse variance matrix to
the regression functions. As more often the case in C/C++ this was
related to pointers ;-).

I think I've fixed the problem in SVN r.852. The test script now passes
without problems on 64bit platforms.

I'd really appreciate it if others could confirm that the new code also
works on their machines (32 or 64bit). If someone has some time on their
hands it may be good to compare the output of the 5 SNP/500 people
example dataset with regression done in another package (R?).



Thanks,

Lennart.


On 13-03-12 22:41, L.C. Karssen wrote:
> Dear list,
> 
> A quick progress report on this bug: I just found two older versions of
> ProbABEL (v0.1-8 and v0.1-9b) in one of my directories. Both were
> compiled under CentOS 64 bit. Both fail the example_mms.sh script, so
> I'm pretty confident now that this bug was not introduced recently.
> 
> Strangly enough the values of the results differ. For example, this is
> the output of the same check as in my first post:
> < rs735579,A,B,0.5847,0.5847,0.5847,0.5847,491,0.534623,1.63067,0.488552
> < rs9088604,A,B,0.5847,0.5847,0.5847,0.5847,497,0.435614,-553.621,1.12808
> < rs1413801,A,B,0.5847,0.5847,0.5847,0.5847,492,0.311992,-6.1979,0.576774
> < rs4911638,A,B,0.5847,0.5847,0.5847,0.5847,496,0.150202,75.6816,0.592895
> ---
>> rs735579,A,B,0.5847,0.5847,0.5847,0.5847,491,0.534623,1.64017,0.493389
>> rs9088604,A,B,0.5847,0.5847,0.5847,0.5847,497,0.435614,264.642,0.778273
>> rs1413801,A,B,0.5847,0.5847,0.5847,0.5847,492,0.311992,-6.19667,0.576738
>> rs4911638,A,B,0.5847,0.5847,0.5847,0.5847,496,0.150202,75.9757,0.592967
> 
> In this case the output of the filevector run does not result in zeroes
> in the second line (although the betas and se_betas still differ between
> filevector and non-filevector files).
> 
> I also found a compiled version of ProbABEL 0.1-3, but that version is
> from the pre-filevector era. Also I noticed that the dose file was
> different from the one in 0.1-9b, so the results are not comparable.
> 
> 
> Lennart.
> 
> On 06-03-12 19:51, Yury Aulchenko wrote:
>> I get apparently the same using Debian 64 bit running under VirtualBox
>> in Mac OS (results attached)
>>
>> I understand that Debian/Ubuntu are related so probably this can not be
>> considered totally independent check. Or am I wrong?
>>
>> Yurii
>>
>>
>>
>> -------------------------------------------------------
>> Yurii Aulchenko, PhD, Dr. Habil.
>> Independent researcher and consultant
>> yurii [dot] aulchenko [at] gmail [dot] com
>>
>> On Mar 4, 2012, at 10:07 PM, L.C. Karssen wrote:
>>
>>> Dear all,
>>>
>>> While preparing (yet again) to make a release of ProbABEL I ran into the
>>> following problem: running the test suite (make check) on my 64 bit
>>> Ubuntu 11.10 machine results in different output for the --mmscore tests
>>> (examples/example_mms.sh), the others (I haven't tried the cox test yet
>>> as it takes several hours) pass.
>>>
>>> See the attached file for the complete output but as you can see in the
>>> following few lines of diff output, the difference is sometimes a few
>>> decimals, but in another line I simply get zeroes for beta and se_beta
>>> in the filevector output:
>>>
>>> < rs735579,A,B,0.5847,0.5847,0.5847,0.5847,491,0.534623,1.63067,0.488552
>>> < rs9088604,A,B,0.5847,0.5847,0.5847,0.5847,497,0.435614,-553.621,1.12808
>>> < rs1413801,A,B,0.5847,0.5847,0.5847,0.5847,492,0.311992,-6.1979,0.576774
>>> < rs4911638,A,B,0.5847,0.5847,0.5847,0.5847,496,0.150202,75.6816,0.592895
>>> ---
>>>> rs735579,A,B,0.5847,0.5847,0.5847,0.5847,491,0.534623,1.66126,0.495227
>>>> rs9088604,A,B,0.5847,0.5847,0.5847,0.5847,497,0.435614,0,0
>>>> rs1413801,A,B,0.5847,0.5847,0.5847,0.5847,492,0.311992,-6.19776,0.576737
>>>> rs4911638,A,B,0.5847,0.5847,0.5847,0.5847,496,0.150202,75.8228,0.59293
>>>
>>>
>>> Strangely enough, on my 32bit Ubuntu 11.04 laptop all tests always pass.
>>>
>>> Can someone else please run the checks on a 64 bit Linux or other
>>> platform? To make sure you are testing the same version, please use SVN
>>> r.847.
>>>
>>>
>>
> 
> 
> 
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-- 
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dr. L.C. Karssen
Erasmus MC
Department of Epidemiology
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