**560**wrote:

Hi All.

I'm using lmekin (http://cran.r-project.org/web/packages/coxme/coxme.pdf) to evaluate a linear mixed model that takes into account the samples' kinship --in fact my dataset includes related individuals. The model I'm using is quite simple:

Transcript_level ~ covariate + (1|famID)

and I'm passing the kinship matrix, created with `kinship`

(R package kinship2), using the `varlist`

parameter. Specifically, the code I'm using is:

model <- lmekin( Transcript_level ~ covariate + (1|famID), data=df, varlist=kinship.matrix))

Unfortunately the evaluation fails because the Cholesky factorisation can't be performed:

Warning message: In .local(x, ...) : Cholmod warning 'not positive definite' at file ../Cholesky/t_cholmod_rowfac.c, line 431 Error in t(solve(chol(as(vmat, "dsCMatrix"), pivot = FALSE))) : error in evaluating the argument 'x' in selecting a method for function 't': Error in solve(chol(as(vmat, "dsCMatrix"), pivot = FALSE)) : error in evaluating the argument 'a' in selecting a method for function 'solve': Error in .local(x, ...) : internal_chm_factor: Cholesky factorization failed

I have tried to evaluate the Cholesky decomposition of my kinship matrix using

chol(as(kinship.matrix, "dsCMatrix"), pivot = FALSE)

as highlighted in the code and it works. However, when using the function Matrix::Cholesky, I obtain:

Error in Cholesky(kinship.matrix) :

internal_chm_factor: Cholesky factorization failed In addition: Warning message: In Cholesky(mykin) : Cholmod warning 'not positive definite' at file ../Cholesky/t_cholmod_rowfac.c, line 431

that it seems to me the same error raised by lmekin. Does anyone has any suggestions?

Thanks in advance for your help,

Alessia

Providing a small example of my data is a bit tricky, but, if necessary, I can try.

> sessionInfo()

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:

[1] splines grDevices utils datasets graphics stats methods

[8] base

other attached packages:

[1] coxme_2.2-3 nlme_3.1-118 bdsmatrix_1.3-2 survival_2.37-7

[5] Matrix_1.1-4 Rdym_0.1.0 reshape_0.8.5 ggplot2_1.0.0

loaded via a namespace (and not attached):

[1] colorspace_1.2-4 digest_0.6.4 grid_3.1.1 gtable_0.1.2

[5] lattice_0.20-29 MASS_7.3-35 munsell_0.4.2 plyr_1.8.1

[9] proto_0.3-10 Rcpp_0.11.3 reshape2_1.4 scales_0.2.4

[13] stringr_0.6.2 tools_3.1.1

**21k**• written 5.0 years ago by alesssia •

**560**