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May 27, 2014

Method Comparison

This add-in helps you compare measurement methods according to CLSI guidelines.  It calls various JMP platforms behind the scenes to fit the data and create a variety of graphical and tabular results.


The add-in consists of four primary routines:  Accuracy, Precision, Linearity, and Performance.  The input data table to each of them must be in stacked format, that is, with one row per individual response.  One column must identify the different rows of data corresponding to the different methods used (the Method Identifer column).  Other required columns of data depend on the routine you use. 


To install the add-in, download "Method Comparison.jmpaddin", drag it onto an open JMP window, then click "Install".  


For example analyses, click Add-Ins > Method Comparison > Help after installing the add-in.  The add-in also includes four example data sets: "Compound Comparison", "Peak Expiratory Flow Rate", "Simulated Example", and "Systolic Blood Pressure".   Click Add-Ins > Method Comparison > Example Data to open them.    


Some example screen shots are below.


6635_Accuracy 1.jpg

6636_Accuracy 2.jpg



6639_Performance 1.jpg

6640_Performance 2.jpg




thanks for the add-in for method comparison. I have a question/remark regarding the Bland Altman plot: why is using the Std Error and not the Std Deviation (SD) to calculate the 95% limits of agreement? The use of Std Error is wrong and consequently is giving wrong limits of agreement.


Literature about Bland Altman plot and the use of Std Deviation (SD):


1. Bland JM, Altman DG. Measuring agreement in method comparison studies. Stat Methods Med Res 1999;8:135-60

2. Bland JM, Altman DG. Statistical methods for assessing agreement between two methods of clinical measurement. Int J Nurs Stud 2010;47:931-6

3.Giavarina D. Understanding Bland Altman analysis. Biochemia Medica. 2015;25(2):141-151






What method are you using for the Confidence Intervals for the Passing Bablock intercept and slope?  If it is bootstrap then please specify what type (e.g., 2.5th and 97th percentile of the distribution of the predicted Y from all the bootstrap estimates) or something else.




I have been trying to get a Bland-Altman analysis going but I don't understand what the method comparison is. I am trying to do Bland-Altman between two different PCR methods (two amplicons of a gene) in order to see how they deviate from each other. Thanks!

@sstinca Apologies for the very long delay.    When we switched over to the new JMP Community website somehow I never got notified of your message.   Thanks for the great catch and I just uploaded an update that includes the Bland-Altman limits using standard deviation and a shaded display on the Matched Pairs graph.  Also added the Systolic Blood Pressure data example from their 1999 paper and numbers agree.


@dstokar The limits are based on the original SAS Macro code from Roche in Penzberg, Germany, which implement the method from Passing and Bablok (1983) and do not use the bootstrap.   If you have good evidence the bootstrap works well here please share, and also the JSL code is open so you can see exactly what is going on and modify it as desired.


@juanpahn  Suggest working through the example in the help doc, making sure you understand everything, then try it on your own data.