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

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
jenn
Posts: 1
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

Hi,

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,
Jenn

Return to “GenABEL”

Who is online

Users browsing this forum: Bing [Bot] and 2 guests