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kbroman / qtl

R/qtl: A QTL mapping environment
https://rqtl.org
GNU General Public License v3.0
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Getting an error in fitqtl #75

Closed huangl07 closed 5 years ago

huangl07 commented 5 years ago

dear I have a error when I use fitqtl in scan<-scanone(d,pheno.col=i,model="binary");

it turns out Permutation 1 Error in solve.default(t(Z) %% Z, t(Z) %% X) : Lapack routine dgesv: system is exactly singular: U[3,3] = 0 Calls: fitqtl -> fitqtlengine -> solve -> solve.default In addition: There were 50 or more warnings (use warnings() to see the first 50)

huangl07 commented 5 years ago

when I use makeqtl summary is image

kbroman commented 5 years ago

I would prefer to answer such questions at the R/qtl google group, rather than as an issue. Could you join and post your question there?

Please provide the actual code you’re using, and give more detail about the nature of the data.

The code you mention:

scan<-scanone(d,pheno.col=i,model=“binary”)

doesn’t involve fitqtl in any way, and wouldn’t give the error you mention or produce the output “Permutation 1“.

The error

Error in solve.default(t(Z) %% Z, t(Z) %% X) :
Lapack routine dgesv: system is exactly singular: U[3,3] = 0

would indicate an over-specified model: too many QTL, or possibly one of the possible genotypes being missing.

huangl07 commented 5 years ago

sorry for lating ,My code is fitqtl with get.est=True: itqtl<-fitqtl(cross=d,qtl=qtl,get.est=TRUE)