Warning INFO

[ddrinan]

Matthew,

Hi, I asked previously (in another thread) about warnings, and wanted to double back on it one more time. When running SCAT on a large SNP data set (+6000 loci), I often get the message Warning INFO=4. I've tried to track this down, and best I can tell, it is related to the dpotrf function (computes the Cholesky factorization of a real symmetric positive definite matrix). My understanding is that if INFO=4, then "the leading minor of order 4 is not positive definite, and the factorization could not be completed." (information from here). That being said, I don't fully understand what is being computed and how it would affect the results. Do you have any insight on whether this is a fatal error such that the results can't be trusted? Also, do you have any idea what would cause this error, or more importantly, how do I get around it?

Thanks,
Dan Drinan

[stephens999]

it could be caused if you have some locations very close together?
Possible solution would be to merge locations that are very close.

Difficult to predict what the impact on results would be....my best guess
would be either very little effect or huge effect... so if the results "generally make sense" I would
speculate they are OK.

[ddrinan]

Haha, I understand. We do have some sites that are relatively close. So, I'll play around with combining them. Generally, the results look good. Thanks so much for your help.