EXPERIMENTAL PLAN

Principal Investigator/Program Director Williams,Robert W.

User manual and tutorials

The user manual will be produced and made available online as hypertext and PDF files. The design will resemble the user manual for Map Manager QT (see appendix). However, the online manual for NTB will include interactive tutorials with real data sets. This material will be modeled on the superb ActiveStats statistics tutorial (DataDescription Inc). Feedback from users of Map Manager QT since its release include many questions on the rationale and strategy of QTL mapping rather than the operation of the software. Our online documentation for the NTB will need to teach the critical statistical concepts needed for successful QTL mapping:

Differences between regression methods and maximum-likelihood methods and other software that makes maximum-likelihood methods available

Interpretation of the Haley and Knott likelihood ratio statistic and its relationship to the c2 statistic and to LRS and LOD scores

Multiple hypothesis testing and its effect on the probability of inference errors

Alternative dominance models, alternative epistasis models, choice of background loci, and mapping itself as examples of multiple hypothesis testing

Advantages and limitations of the nonparametric (rank-sum) method

Different strategies of composite interval mapping for linked and unlinked QTLs

Limitations on the ability of any QTL mapping method to resolve closely linked QTLs unless the effect of the QTLs is in the opposite direction

The importance of empirical significance thresholds established by permutation tests and the rationale for different permutation tests

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