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 Problems with sigmoidal fitting - Gompertz model

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T O P I C    R E V I E W
T_Swebocki Posted - 11/23/2022 : 06:58:47 AM
Hello,

I am plotting MIC (Minimum inhibitory concentration) data. Data should be fitted to Gompertz model. Such model exists in OriginPro, however, usually doesn't work.

Example of data:



Error that occurs below:

(1) Parameter Initialization was called.
(2) Parameter Initialization was called.
(3) Parameter Initialization was called.
(4) ---------------Chi-Square---------------
Reduced Chi-sqr = 591.093861463
(5) -----Orthogonal Distance Regression-----
Reduced Chi-sqr = 115.76659027
COD(R^2) = 0.41875347893492
Iterations Performed = 2 
Total Iterations in Session = 2
(6) Fit did not converge - reason unknown.
Fitting was done with weights. Check weighting method and error bar values for possible inconsistencies, or try fitting again with weights turned off.


And this is for every data I use. I noticed that this model is called in OriginPro "SGompertz" and not "Gompertz".

The model in OriginPro seems the same to me as the one that works in other program that I use for plotting:
EQUATION:
M=logMIC - 1/Slope
Y= Bottom + Span*exp(-1*exp(Slope*(X-M)))



I have no idea why the fitting is not working in OriginPro. And that's a pity as I cad (and do!) process every of my data in OriginPro except MIC data...

Can anyone please help me to locate the problem and tell me how to solve it I am not really good at programming etc. and Origin is still after almost 5 years a mystery to me in some aspects... :P
6   L A T E S T    R E P L I E S    (Newest First)
T_Swebocki Posted - 11/24/2022 : 03:34:30 AM
James - thanks! Works exactly as intended!
YimingChen Posted - 11/23/2022 : 5:09:22 PM
You can define the fitting function below to use the original x values:
M=log(MIC) - 1/Slope
Y= Bottom + Span*exp(-1*exp(Slope*(log(X)-M)))

and use MIC instead of logMIC as parameter.

Check the updated fitting function and the project:

https://my.originlab.com/ftp/forum_and_kbase/Images/SGompertz2.zip

T_Swebocki Posted - 11/23/2022 : 2:47:07 PM
Hi James,

Thanks for help.

I have two more questions regarding this fitting function:

1. After fitting, I can see logMIC but not MIC values in the table that appears after fitting is done. Is there anyway to make the table show MIC (so 10^logMIC) also?


2. Is there anyway to automatise the work a little bit? Basically, plots with log scale are not really useful to work (or publish) with this type of data. By using the model you provided I have to manually convert x scale to log (in separate column), then create two plots - one with linear x scale, one with logarithmic. I fit "logarithmic plot" to get MIC value, but then I need to also add fitting curve to a plot with linear scale.

Anyway thank you very, very much for your help! It really helps with my data for PhD!
YimingChen Posted - 11/23/2022 : 2:12:53 PM
You will need to define the derived parameter MIC = 10^logMIC in the Parameter Definition page in Fitting Function Builder (menu Tools->Fitting function Builder). Also to perform the fitting properly, you need to first convert the x values to log(x). Please check the attached project file and the modified fitting function. Thank you.

https://my.originlab.com/ftp/forum_and_kbase/Images/SGompertz.zip

T_Swebocki Posted - 11/23/2022 : 11:58:07 AM
Hello James,

Thanks - it fits perfectly! However, I still need to obtain MIC value for this (see below). A point of intersections of two linear fragments.


Is it possible to obtain coordinates for that point directly into the table?

Thank you in advance!
YimingChen Posted - 11/23/2022 : 09:05:06 AM
The SGompertz function in Origin doesn't have the y offset term. You need to customize the fitting function to include the offset. See the figure below.



Please also find the attached fitting function file. Drag the .fdf file into Origin work space to install it. And try it on your data. You should be able to find the fitting function CustomizedSGompertz under the User Defined category in the NLFit dialog.
https://my.originlab.com/ftp/forum_and_kbase/Images/CustomizedSGompertz.FDF

James

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