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perishky / meffil

Efficient algorithms for analyzing DNA methylation data.
Artistic License 2.0
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error in meffil.ewas #6

Closed guhem closed 5 years ago

guhem commented 6 years ago

Hey, I'm getting an error running the following command: set.seed(5) ewas.ret <- meffil.ewas(norm.beta, variable=phen[,2], covariates=covs, isva=F)

Error message: Error in sove.default(t( %*% mod) : System is computationally singular: reciprocal condition number = 1.9905e-43 Calls: meffil.ewas -> sva -> num.sv -> solve -> solve.default Execution halted

Anyone who what this error message means?

perishky commented 6 years ago

The problem is with the input to sva (phen[,2] and covs). Most likely you have two or more categorical variables that together define sample groups with too few samples to fit the model.