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Stop when encountering a NaN #161

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pjotrp opened this issue Jul 23, 2018 · 1 comment
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Stop when encountering a NaN #161

pjotrp opened this issue Jul 23, 2018 · 1 comment

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@pjotrp
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pjotrp commented Jul 23, 2018

When we see:

 ## REMLE estimate for Ve in the null model:
 2.14138e-05
 -3.21985e-06    1.68684e-06
 -1.21203e-05    -1.80521e-06    1.82497e-05
 ## se(Ve):
 1.72819e-05
 5.62131e-06     2.21151e-06
 1.07007e-05     -nan    1.17464e-05

there is a nan which suggests the results are unstable. We are
dealing with round-off errors most likely (division of values close to zero).

Shouldn't gemma stop processing when it detects such a situation.
In fact I want to suggest GEMMA stops at any point a nan gets
introduced anywhere because it implies we are operating at machine
boundaries and results can not be trusted.

Xiang wrote:

Yes, I agree. I have seen this nan error a few times before, in either the Ve or Vg estimates. Sometimes better phenotype normalization can help preventing the error, but sometimes doesn't -- and in those cases I couldn't figure out why. But I agree it makes sense to stop processing when it detects such an error.

@pjotrp pjotrp self-assigned this Jul 23, 2018
@pjotrp pjotrp added this to the 0.99 release milestone Jul 23, 2018
pjotrp added a commit to genenetwork/GEMMA that referenced this issue Jul 27, 2018
When using the -check function (the default) it is enabled for Kinship
computation and LM/LMM up to individual SNP computation. This means
there can no longer be NaN values for matrices that are reused for every
SNP, but it is possible to have NaN for individual SNPs.

Fixes genetics-statistics#161
@pjotrp
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pjotrp commented Aug 25, 2018

We now have default hardware detection of FP out of boundary errors on Intel x64. Releasing soon.

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