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## 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.
The text was updated successfully, but these errors were encountered:
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.
Fixesgenetics-statistics#161
When we see:
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.
The text was updated successfully, but these errors were encountered: