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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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The additive effects of some markers is NA in the bcsft population #59

Closed jingxianyu closed 7 years ago

jingxianyu commented 7 years ago

Hello, I use the CIM algorithm for localization,my population type if BC4F3,but the dditive effects of some markers is NA,and I can't find the reason, I ask for help to explain it,Thank you!

kbroman commented 7 years ago

We need more information: further details on your data, and the code you're using.

jingxianyu commented 7 years ago

This is the code and data I used. data_code.zip

kbroman commented 7 years ago

Can you explain in more detail what the problem is?

jingxianyu commented 7 years ago

This is the result of some markers, in the result,the dditive effects of some markers are NA, but some are calculated.I can't find the reason. test.result.zip

kbroman commented 7 years ago

The NAs seem to come from cases where the BB genotypes is entirely absent. You might get somewhat better results by using a large value for n.draws when calling sim.geno(), but I think generally you're going to have difficulty getting estimates of the additive and dominance effects given the segregation pattern in the cross.