Thank you, I'll try it!
On Thu, Mar 18, 2021 at 9:46 PM Rui Barradas wrote:
>
> Hello,
>
> Maybe a bit late but there is a contributed package [1] for quantitative
> PCR fitting non-linear models with the Levenberg-Marquardt algorithm.
>
> estim and vector R below are your model and your fitted v
Hello,
Maybe a bit late but there is a contributed package [1] for quantitative
PCR fitting non-linear models with the Levenberg-Marquardt algorithm.
estim and vector R below are your model and your fitted values vector.
The RMSE of this fit is smaller than your model's.
Isn't this simpler
It worked. I re-written the equation as:
```
rutledge_param <- function(p, x, y) ( (p$M / ( 1 + exp(-(x-p$m)/p$s))
) + p$B ) - y
```
and used Desmos to estimate the slope, so:
```
estim <- nls.lm(par = list(m = halfCycle, s = 2.77, M = MaxFluo, B = high[1]),
fn = rutledge_param, x = 1:4
Just an update:
I tried with desmos and the fitting looks good. Desmos calculated the
parameters as:
Fmax = 11839.8
Chalf = 27.1102 (with matches with my estimate of 27 cycles)
k = 2.76798
Fb = -138.864
I forced R to accept the right parameters using a single named list
and re-written the formula (
Hello,
the negative data comes from the machine. Probably I should use raw
data directly, although in the paper this requirement is not reported.
The p$x was a typo. Now I corrected it and I got this error:
```
> rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(x-p$m)/p$s))) + p$B)
> - y
> rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(p$x-p$m)/p$s))) +
> p$B) - y
Did you mean that p$x to be just x? As is, this returns numeric(0)
for the p that nls.lm gives it because p$x is NULL and NULL-aNumber is
numeric().
-Bill
On Sun, Mar 14, 2021 at 9:46 AM Luigi Marongiu wro
Do the negative values in your data make any sense? Note that if Fb must be
>0, Fc must be also.
But I have *not* examined your code/equations in detail, so feel free to
ignore if this is irrelevant.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
Hello,
I would like to use the Rutledge equation
(https://pubmed.ncbi.nlm.nih.gov/15601990/) to model PCR data. The
equation is:
Fc = Fmax / (1+exp(-(C-Chalf)/k)) + Fb
I defined the equation and another that subtracts the values from the
expectations. I used minpack.lm to get the parameters, but I
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