Hello the community,
We are facing some issue in our inflection point calculation for a nonlinear 4P Rodbard fitting.
The model is basic:
X: concentration [nM]
Y: %Specific Killing
By: samples
I usually run this on JMP, but other team members in our departement are using the service of ou bio-informatitian and she used the concentration in pM.
At first sight, no issue, only a factor of 1000 should be the difference. However, we found that for some fitting, she do not have any issue but I observed different results on JMP.
Here is an example:
Concentration [nM] |
Concentration [pM] |
Specific Killing [%] |
20 |
20000 |
103.2 |
2 |
2000 |
103.5 |
0.2 |
200 |
102.6 |
0.02 |
20 |
104.9 |
0.002 |
2 |
99.9 |
0.0002 |
0.2 |
-5.0 |
0.00002 |
0.02 |
13.3 |
0.000002 |
0.002 |
9.2 |
2E-07 |
0.0002 |
0.3 |
2E-08 |
0.00002 |
6.1 |
And here my model results
Using x as Concentration [nM]
Parameter |
Estimate |
Std Error |
Wald ChiSquare |
Prob > ChiSquare |
Lower 95% |
Upper 95% |
Growth Rate |
-5.39 |
282.61 |
0.00 |
0.98 |
-559.29 |
548.50 |
Inflection Point |
0.001096 |
0.03 |
0.00 |
0.97 |
-0.07 |
0.07 |
Lower Asymptote |
4.77 |
2.98 |
2.57 |
0.11 |
-1.07 |
10.61 |
Upper Asymptote |
103.55 |
2.98 |
1209.02 |
<.0001 |
97.71 |
109.39
|
Using x as Concentration [pM]
Parameter |
Estimate |
Std Error |
Wald ChiSquare |
Prob > ChiSquare |
Lower 95% |
Upper 95% |
Growth Rate |
-6.76 |
6445.81 |
0.00 |
1.00 |
-12640.32 |
12626.80 |
Inflection Point |
1.2354 |
567.78 |
0.00 |
1.00 |
-1111.60 |
1114.07 |
Lower Asymptote |
4.77 |
2.98 |
2.57 |
0.11 |
-1.06 |
10.61 |
Upper Asymptote |
103.54 |
2.98 |
1209.97 |
<.0001 |
97.71 |
109.38 |
As you can see, there is not just a 1000 fold differences in the inflection point (and other differences for example the growth rate).
Do you know why we have such difference ? For almost all of our samples there is no differences it is only few of them,
We also see different value if are running a 4PL with variable slope on Prism on with R using our bio-info sript (when is it usually similar).
Can you help us ?
Thanks in advance for your help