topic Re: creating a mean table with p-vaue in Discussions

creating a mean table with p-vaue

mpatpc — Tue, 09 May 2017 20:58:27 GMT

Looking to create a data output table from an comparison of means analysis that shows the mean of each atrribute by sample with p-value to show if the mean values are significantly different. How can I do that in JMP? I can generate a table using tabulate but cant seem to add p-value which is generated during hte one way anova analysis

Re: creating a mean table with p-vaue

txnelson — Tue, 09 May 2017 21:28:10 GMT

If you go to

Analyze==>Screening==>Response Screening

You can enter in all of your Y variables, and you X variable(s) and it will generate a data table with your results, including the p-values

Re: creating a mean table with p-vaue

Mark_Bailey — Tue, 09 May 2017 21:49:05 GMT

Use the Oneway platform. Start by selecting Analyze > Fit Y by X. I assume that you have a numeric variable stored in a data column using the continuous modeling type for the Y role. I also assume that you have a categorical variable in a data column using the nominal modeling type. Put that column in the X role.

Click the red triangle next to Oneway and select Compare Means > Tukey-Kramer. You will find the answer several different ways. The last report shows what you want. Remember that you can right-click on this last report and select Make Into Data Table if you need to do something else with results.

Re: creating a mean table with p-vaue

Kevin_Anderson — Wed, 10 May 2017 17:47:42 GMT

Perhaps I'm overly-sensitive, but since this sounds a bit like p-hacking to me, I thought it might help to post the American Statistical Association position paper on the proper use of p-values.

Re: creating a mean table with p-vaue

mpatpc — Wed, 10 May 2017 21:20:28 GMT

I can generate the table this way but if I have multiple one way analysis how do I get a table for each.

Example: I have sample 1 (control) , sample 2 and sample 3. I recorded dimension data for length, width, and height.

I am comparing if sample 1 (control) is significantly different than sample 2 and 3 for each length, width and height.

So when I create the one way it is just for sample 1, 2 & 3 for length. How can I create a table with p-value for length, width and height. Do I need to go to the red triangle for each dimension, compare mean then create the table? This seems inefficient. Could I just use the tabulate function to create the table of means then in the data table add a formula to create the p-value?

Re: creating a mean table with p-vaue

Jeff_Perkinson — Wed, 10 May 2017 21:35:44 GMT

You can broadcast the Compare Means command across your report and then use Make Combined Data Table to make one data table from all the individual report tables.

Start with Fit Y by X using sample as X and length, width, height as Y.

Then, in the report, hold the Ctrl key (Windows) or Command key (Mac) down and choose Compare Means -> All Pairs, Tukey HSD.

Then in the report table that contains the p-Values, right click and choose Make Combined Data Table.

That gets you one data table with all the p-values.

Re: creating a mean table with p-vaue

msleo — Thu, 06 Jul 2017 06:01:22 GMT

thanks for the suggestion. Is there a way to access the output table of Response Screening from jmp script?

I would like to iterate through the table and pick up all the row numbers that have a RSquared > 0.95.

This output table doesnt seem to be the current data table.

Re: creating a mean table with p-vaue

txnelson — Thu, 06 Jul 2017 09:30:00 GMT

Here is an example of how to do that taken from the Scripting Index

Help==>Scripting Index==>Response Screening==>Get PValues

Names Default To Here( 1 );
Open( "$Sample_Data/Probe.jmp" );
obj =
Response Screening(
	X( :Process ),
	Y( Eval( 8 :: 394 ) ),
	Save Outlier Indicator
);
dtOut = obj << Get PValues ;
show( dtOut );
dtOut << Select Where( :RSquare > .95 );

I modified it very slightly, to add the pointer to the "PValues" data table which you can then use to do the selection of the RSquare values. I do recomment that you examine the FDR Logworth values. When doing so many tests, the FDR Logworth will help you determine which of the tests are real, and which are due to alpha slipping.

Re: creating a mean table with p-vaue

msleo — Wed, 12 Jul 2017 02:35:50 GMT

Thank you, FDR logworth seems to be useful.
Actually my data set has about 6000 columns all with p-value < 0.01 and many with a significant FDR logworth. However, some of the columns correlate to other columns with RSquare > 0.95 (similar test results). So currenly I'm running response screening of all columns vs all columns, grouping those columns that correlate with RSquare > 0.95 and then keeping just 1 of the correlating columns per group. It does take a few hours (~1000 rows) to run the script though for a decent reduction in number of columns.

Would be great if there is a faster way to group correlating columns together and then just keep 1 column per group. Pls share if there's a better way to do this.

Re: creating a mean table with p-vaue

txnelson — Wed, 12 Jul 2017 02:42:04 GMT

You could create a correlation matrix using

Analyze==>Multivariate Methods==>Multivariate

or use Prinicpal Components analysis

Analyze==:Multivariate Methods==>Principal Components

Re: creating a mean table with p-vaue

Mark_Bailey — Wed, 12 Jul 2017 11:45:18 GMT

The procedure that you are looking for is called 'variable clustering.' The Cluster Variables command in the Analyze menu will launch the JMP platform for this purpose.

Please see Help > Books > Multivariate Methods > Chapter 11: Cluster Variables for more information.