Re: [Rqtl-disc] Using the marker map of F2 for QTL mapping in the F3 generation?

[Karl Broman]

Dear Stefan,

R/qtl can't formally handle F3 data. The simplest thing would be to focus solely on the F3 genotypes and phenotypes, treating them as if they were a regular F2. And so I would use the map estimated via the F3 data.

But I'd be concerned about F3 sibships...that there would be groups of more closely related individuals, not taken into account if one treated the F3 individuals as if they were a simple F2.

karl

On Feb 4, 2010, at 7:29 AM, Stefan wrote:

> Dear Prof. Broman and all R/qtl users,
>
> i set up a mouse intercross experiment. The F2 was genotyped but only
> the F3 was genotyped and also phenotyped.
>
> I know R/qtl is not meant to be used for F3 data, but I am interested
> in finding QTLs in the F3 and since its crucial to have an exact map,
> I was asking myself, if I could/should/must use the marker map of the
> F2 and replace the original F3 map, which could also be created?
>
> http://s825.photobucket.com/albums/zz176/sonnenflecken/?action=view&current=100204_VGLF2undF3.png
>
> Sincerely
> Stefan Kärst
>
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[Stefan]

Dear Karl,

Thank you for your advice. I will do so.

Take care
Stefan