high LOD in empty spaces

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Vianey B.E

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Apr 15, 2021, 12:37:22 PMApr 15
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Dear Karl

I am working with a 4-way cross. I have got some QTL using scanone (em method) but when I take a closer look I notice that some QTLs have high LOD values in areas without any marker. I would like to understand what is happening here.
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Karl Broman

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Apr 15, 2021, 12:41:31 PMApr 15
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Take a look at chapter 4 of the R/qtl book.


karl

Vianey B.E

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Apr 15, 2021, 4:28:10 PMApr 15
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Thanks, Karl. I understand better what is happening. I checked manually the data and used the effectplot function to confirm if the involved markers have similar behaviour (phenotype vs genotype) and it was as the book described.
I was wondering if there is a limitation in the size of the gaps of missing information and what precautions should be taken when this kind of QTL appear?  Currently, I am using a step size of 0.5 cM

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Karl Broman

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Apr 15, 2021, 9:59:38 PMApr 15
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the marker gaps you have don’t look big, but you haven’t said what sort of cross this is.

the step argument just concerns where calculations are done. step=0 means just do calculations at the markers, but otherwise that choice shouldn’t influence things.

the usual solutions are to find the source of the problem (skewed phenotype?) and fix that (take logs?), or to switch to a different method, like haley-knott regression or imputation.

karl

Vianey B.E

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Apr 20, 2021, 8:55:09 AMApr 20
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Thanks for your reply, Karl
It is a 4-way cross, two heterozygous diploid parents with contrasting phenotypes. 
I have other QTLs with gaps of 20cM more or less, but checking the phenotypes I have found that those QTLs appear in skewed phenotypes. I will try your suggestions.  

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