try option llfun='polylik' & In sqrt(eigValInvSig) : NaNs

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Joined: Fri Oct 28, 2011 3:42 pm

try option llfun='polylik' & In sqrt(eigValInvSig) : NaNs

Postby jenn » Fri Oct 28, 2011 4:38 pm


I am using the polygenic function in GenABEL to test candidate SNPs in a population isolate (n=~800). There are no missing values in any of the covariates, and with: summary(y2$convFGLS), I get TRUE=1, NA's=0 for all models. I constantly get a warning message: In polygenic(....): some eigenvalues <=0, taking ABS for det; try option llfun='polylik'. The GenABEL manual states that llfun='polylik' is an option but not recommended, is this simply due to the differences in processing times?

I am using the loglik of nested models to determine the effect of the SNP and have tested a few outcomes. Eg. if I compare
y1 <- polygenic(y~Age+Sex+SNP+pc1+pc2+pc3, kin=gkin, data=df1, quiet=T) and
y0 <- polygenic(y~Age+Sex+pc1+pc2+pc3, kin=gkin, data=df1, quiet=T), with
y2 <- polygenic(y~Age+Sex+SNP+pc1+pc2+pc3, kin=gkin, data=df1, quiet=T, llfun='polylik) and
y0 <- polygenic(y~Age+Sex+pc1+pc2+pc3, kin=gkin, data=df1, quiet=T, llfun='polylik),
I get identical p-values. Given that I had the same results (and have a lot of analyses to run) I am currently ignoring this warning, but should I be concerned?

On occasion I also get another warning message: In sqrt(eigValInvSig) : NaNs produced. This seems to be associated with a smaller population size and affects the loglik values, and therefore prevents me from comparing the full and null models and getting a p-value. For example when I analyse my population in full and then by sex, I will only get the warning message for the males for some outcomes. Is there anything I can do to avoid this?

I would appreciate any advice. Thanks,

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