topic Re: Calculate and add dose range based on provided values in Discussions

Calculate and add dose range based on provided values

Pim — Fri, 20 Dec 2024 10:57:27 GMT

I am building a script to import and analyze raw sample data generated in a bioassay.

For this, it is necessary to identify reference data and sample data and to set the corresponding dose range.

In my script I included a ‘sample info’ pop-up window in which operators can identify sample locations (Row x + x) and enter the desired dose-range for these samples. And this is where my struggle comes in!

The sample names are correctly added to the data table, but how do I get the dose points based on entered values in there?

The script should be able to calculate each dose point based on a starting concentration and dilution factor.

What I want it to look like (see 'Dose' column, manually entered for this example):

Any suggestions?

I am working in JMP 18, my script for the sample info pop up so far:

nw = New Window( "Sample info", << Modal,
	H List Box(
		Panel Box( "Enter Sample names",
			V List Box(
				Text Box( "Row A+E" ),
				AE = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row B+F" ),
				BF = val2 = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row C+G" ),
				CG = val3 = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row D+H" ),
				DH = val4 = Text Edit Box( "", << Set Width( 200 ) );
			)
		),
	
		Spacer Box( Size( 10, 10 ) ),
	
		V List Box(
			Panel Box("Calculate dosepoints",
				V List Box(
					Text Box( "Start Conc. (ng/mL)" ),
					Conc = Number Edit Box(  ),
					Text Box( "n Dosepoints" ),
					nDP = Number Edit Box( 12 ),
					Text Box( "Factor" ),
					xF = Number Edit Box( 0.2 ),
				)
			),
		
			Spacer Box( Size( , 8 ) ),

			H List Box( 
			
				Spacer Box( Size( 77, 1 ) ),
			
				Button Box("Ok",
				val1 = AE << Get text ();
				val2 = BF << Get text ();
				val3 = CG << Get text ();
				val4 = DH << Get text ();
				val5 = Conc << Get ();
				val6 = nDP << Get ();
				val7 = xF << Get ();
				
					Current Data Table() << New Column( "Sample", Character, "Nominal", 
						Formula( 
							Match( :Row,
								"A", val1,
								"E", val1,
								"B", val2,
								"F", val2,
								"C", val3,
								"G", val3,
								"D", val4,
								"H", val4
							)
						)
					);
					
					Current Data Table() << New Column( "Dose", Character, "Nominal", 
						//Formula( ????

						//	)

					),
				)
			)
		)
	)
);

I have added an example Data table in which the above script should work.

Re: Calculate and add dose range based on provided values

jthi — Fri, 20 Dec 2024 12:02:24 GMT

Maybe something like this

Eval(EvalExpr(
	dt << New Column("R", Numeric, Continuous, Formula(
		Expr(start_conc)/ Expr(factor) ^ (Col Number(:Sample, :Sample) - Col Cumulative Sum(1, :Sample))
	));	
));

Re: Calculate and add dose range based on provided values

Pim — Fri, 20 Dec 2024 12:26:52 GMT

Almost!
I adapted your script a little and was able to calculate the right dose range for 1 of the replicates! (see attachment). The other replicate should have the same values (i.e. 20.000 - 0.0004 ) but instead keeps dividing the last result of replicate 2.

So, for Sample 'RS', located in Row A (replicate 1) and E (replicate 2), Row E values range from the desired 20.000 to 0.0004 range, but for Row A the range is 0.0008 - 1.67e-12.

nw = New Window( "Sample info", << Modal,
	H List Box(
		Panel Box( "Enter Sample names",
			V List Box(
				Text Box( "Row A+E" ),
				AE = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row B+F" ),
				BF = val2 = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row C+G" ),
				CG = val3 = Text Edit Box( "", << Set Width( 200 ) ),
				Text Box( "Row D+H" ),
				DH = val4 = Text Edit Box( "", << Set Width( 200 ) );
			)
		),
	
		Spacer Box( Size( 10, 10 ) ),
	
		V List Box(
			Panel Box("Calculate dosepoints",
				V List Box(
					Text Box( "Start Conc. (ng/mL)" ),
					Conc = Number Edit Box(  ),
					Text Box( "n Dosepoints" ),
					nDP = Number Edit Box( 12 ),
					Text Box( "Factor" ),
					xF = Number Edit Box( 0.2 ),
				)
			),
		
			Spacer Box( Size( , 8 ) ),

			H List Box( 
			
				Spacer Box( Size( 77, 1 ) ),
			
				Button Box("Ok",
				val1 = AE << Get text ();
				val2 = BF << Get text ();
				val3 = CG << Get text ();
				val4 = DH << Get text ();
				val5 = Conc << Get ();
				val6 = nDP << Get ();
				val7 = xF << Get ();
				
					Current Data Table() << New Column( "Sample", Character, "Nominal", 
						Formula( 
							Match( :Row,
								"A", val1,
								"E", val1,
								"B", val2,
								"F", val2,
								"C", val3,
								"G", val3,
								"D", val4,
								"H", val4
							)
						)
					);
					
Eval(
	EvalExpr(
		Current Data Table() << New Column( "R", Numeric, Continuous,
			Formula(
				Expr(val5) / Expr(val7) ^ ( Col Number( :Sample, :Sample ) - Col Cumulative Sum( 1, :Sample ))
			)
		);	
	)
);

				)
			)
		)
	)
);

Re: Calculate and add dose range based on provided values

jthi — Fri, 20 Dec 2024 12:40:01 GMT

You have to add additional grouping to Col Number and Col Cumulative Sum (Row might work for example)

20000 / 5 ^ (Col Number(:Sample, :Sample, :Row) - Col Cumulative Sum(1, :Sample, :Row))

Re: Calculate and add dose range based on provided values

Pim — Fri, 20 Dec 2024 12:43:16 GMT

Yes, this works perfectly! Thank you!