[GenABEL-dev] t-statistic, p-values from source data

[Frank, Alvaro Jesus]

Hi All,

I apologize for any noise this may produce.
Adding p-values, std erros and by default t-stests/statistics to omicabelnomm has been more than difficult.
The reason for this is that I cannot seem to find a unified consensus of what the user wants in terms of statistics.
Some do t-stat on X, others on Y, but all expect a p-val from the linear regression that not even them know where it comes from. I have good handling of all formulas needed, but the final-pvalue requires a t-test from a sample data.
Is that sample data the residual of the Y-XB or just the produced factors B or simply the data X or Y?
Some of this make sense while others make no sense at all.

Another concern of mine is that some of the data used may not have enough significant digits beyond the 3rd digit. IF the p-value is supposed to come from the residual, this residual could be good or even bad depending on the conditioning of X. If the residual is very close to machine precision, using it for a pvalue becomes not at all advisable because of significant digits, or am I wrong about this?

I feel I am missing something in terms of workflow or formulas or even purpose/usage of the regression and the p-value.

Any help would be appreciated.

-Alvaro

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