topic Re: change p-value output format in preferences in Discussions

change p-value output format in preferences

l_yampolsky — Sun, 11 Mar 2018 15:06:27 GMT

Simple question. I understand the reasons why reporting p<0.0001 as "<0.0001"; I also understand how to change the number format in individual outputs. However, for some downtream analyses (like FDR calculation) it is necessary to have the exact p-value AND it is difficult to change format in a large output with thousands of tests. Is there a way to change the preference for p-value output system-wide? Or at least for each analysis separately, but before the output has been generated?

Thanks!

Re: change p-value output format in preferences

Mark_Bailey — Sun, 11 Mar 2018 19:04:43 GMT

If you will be calculating FDR then you will have a lot of p-values. A script can extract the p-vaue. The format only affects the display of this value. The value extracted will be full-precision regardless of the format.

Re: change p-value output format in preferences

l_yampolsky — Mon, 12 Mar 2018 00:12:28 GMT

Could you post an example of a script that extracts p-values? I usually do this by copying the output into a table and parsing it, works ok. But yes, sure, a script would be easier.

Re: change p-value output format in preferences

Mark_Bailey — Mon, 12 Mar 2018 13:01:19 GMT

This example illustrates the basic steps. You could extend it in many ways to suit a particular case.

// set namespace
Names Default to Here( 1 );

// open data set
dt = Open( "$SAMPLE_DATA/Big Class.jmp" );

// launch platform and estimate parameters
biv = dt << Bivariate( Y( :weight ), X( :height ), Fit Line );

// obtain reference to report layer
biv rep = biv << Report;

// obtain p-value for parameter estimate from report layer
pVal = biv rep["Parameter Estimates"][NumberColBox("Prob>|t|")] << Get( 2 );

Re: change p-value output format in preferences

l_yampolsky — Mon, 12 Mar 2018 14:54:17 GMT

Thanks, this is really helpful!