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snpMatrix package is quite nice (read.plink())

Maybe glmer(cbind(abnormal, normal) ~ treatment*genotype + (1|batch), data=x, family=binomial())

Sewall Wright used an ordinal model for toes, IIRC ;). It might be more stable. Cheers, David Duffy,

On Tue, 20 Aug 2013, Ben Bolker wrote: > "hmm, that looks complicated..." Now was that "HMM, that looks complicated", or "hglm, that looks complicated" ???

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In finadata.txt. you have ANIMID 3178 in twice, once as offspring of 1156 and 3104, and later as offspring of 1156 and 3065 (mergped as only the latter).

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francesca casalino <francy.casalino at gmail.com> asked: > > Does anyone know how to find the reference allele used for genetic > associations ran in snpStats? > A is ref allele, B is risk allele.

You need to provide boring details like "sessionInfo()" on old and new machines, so we can see which versions of the packages you actually have installed, and whether your locale is weird...

On Tue, 13 Nov 2012, Ben Bolker wrote: > * you could try bootstrapping or permutation testing (being careful > to respect the grouping structure of the data lmPerm package may be useful for this

On Mon, 6 Feb 2012, Kevin Spring wrote: > I can't do it this way because the boot function only allows for one data > set to be inputted. So you tried one combined dataset and subset?

On Thu, 17 Feb 2011, Quincy Elamore wrote: > pilotstudy.glm<-glmer(log.error~true_percentage + Distance + Angle +(1|Subject), > data=pilotstudy) This looks sensible to me, FWIW. You might say lmer rather than glmer. Cheers, David Duffy.

> I am interested in simulating 10,000 2 x 3 tables for SNPs data with the > Hardy Weinberg formulation. Is there a quick way to do this? I am assuming > that the minor allelle frequency is uniform in (0.05...

I have not done any comparisons versus other programs, but: https://mran.microsoft.com/package/HMMEsolver where the algorithm is described in Kim (2017) A Fast Algorithm for Solving Henderson's Mixed Model Equation https://arxiv.org/pdf/1710.09663

What did you get from MCMCglmm(...family="gaussian")? -- | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia...

Cristian Pattaro asked: > is there a automatic method to obtain Odds Ratio estimates and their > confidence intervals from a GLM Logistic model? something like: oddsr<-function(x) { require(MASS) round(exp(cbind(Odds.Ratio=coef(x), confint(x))),3) } oddsr...

On Mon, 9 Dec 2013, marieline gentes wrote: > I simply want to report the fact that year (categorical, three levels) > What is the proper way to do this ? Should I not be using glmmPQL ? You could use Anova() from John...

Before anyone else says it -- upgrade your version of R and try again. Cheers, David Duffy. -- | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical...

Trenkler, Dietrich said: > > I found the following strange behavior using qnorm() and pnorm(): > > > x<-8.21;x-qnorm(pnorm(x)) > [1] 0.0004638484 > > x<-8.28;x-qnorm(pnorm(x)) > [1] 0.07046385 > > x<-8.29;x-qnorm(pnorm(x...