mlreg error zero elements in diagonal

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Joined: Wed Apr 08, 2015 2:22 pm

mlreg error zero elements in diagonal

Postby Annemieke » Mon Oct 19, 2015 12:14 pm

Hi all,
I would like to do logistic regression analysis in GenABEL for about 300 cases and 5000 controls for about 200,000 SNPs, for which I use the following command;

logreg_all<-mlreg(outcome~sex, data_set, gtmode = "additive", trait.type = "binomial", propPs = 1)

However, I get an error:
#Error in mlreg(outcome ~ sex, data_set, gtmode = "additive", trait.type = "binomial", :
# invert: zero elements in diagonal

My outcome is 1/0, I would like to test the additive effect of the SNPs.
I already selected SNPs with MAF (minor allele frequency (summary$Q.2)) >0 and high call rate PER outcome group (or is monomorph allowed in one of the two groups?)

The error does not occur when I make a selection of SNPs for which also the frequency of heterozygotes and of homozygotes for the minor allele is larger than 0 in both outcome groups (summary_cases$P.12>0 & summary_cases$P.22>0 & summary_controls$P.12>0 summary_controls$P.22>0).
However, I don't want to exclude these SNPs, and it seems that my SNPs are tested as a categorial variable (where you can not miss a category), instead of as a integer (0,1 and 2)?

Can anyone help me?
Many thanks in advance!

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