[R] Failure in predicting parameters
Luigi Marongiu
m@rong|u@|u|g| @end|ng |rom gm@||@com
Tue Mar 16 08:29:09 CET 2021
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 (it was a bit unclear in the paper):
```
rutledge <- function(p, x) {
m = p$half_fluorescence
s = p$slope
M = p$max_fluorescence
B = p$back_fluorescence
y = (M / (1+exp( -((x-m)/s) )) ) + B
return(y)
}
```
but when I apply it I get a funny graph:
```
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)
```
On Mon, Mar 15, 2021 at 7:39 AM Luigi Marongiu <marongiu.luigi using gmail.com> wrote:
>
> 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$B) - y
> > estim <- nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B = high[1]),
> + fn = rutledge_param, x = 1:45, y = high)
> Error in dimnames(x) <- dn :
> length of 'dimnames' [2] not equal to array extent
> ```
> Probably because 'slopes' is a vector instead of a scalar. Since the
> slope is changing, I don't think is right to use a scalar, but I tried
> and I got:
> ```
> > estim <- nls.lm(par = list(m = halfFluo, s = 1, M = MaxFluo, B = high[1]),
> + fn = rutledge_param, x = 1:45, y = high)
> > estim
> Nonlinear regression via the Levenberg-Marquardt algorithm
> parameter estimates: 6010.94, 1, 12021.88, 4700.49288888889
> residual sum-of-squares: 1.14e+09
> reason terminated: Relative error in the sum of squares is at most `ftol'.
> ```
> The values reported are the same I used at the beginning apart from
> the last (the background parameter) which is 4700 instead of zero. If
> I plug it, I get an L shaped plot that is worse than that at the
> beginning:
> ```
> after = init = rutledge(halfFluo, 1, MaxFluo, 4700.49288888889, high)
> points(1:45, after, type="l", col="blue")
> ```
> What did I get wrong here?
> Thanks
>
> On Sun, Mar 14, 2021 at 8:05 PM Bill Dunlap <williamwdunlap using gmail.com> wrote:
> >
> > > rutledge_param <- function(p, x, y) ((p$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 <marongiu.luigi using gmail.com> wrote:
> > >
> > > 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 got an
> > > error:
> > > ```
> > >
> > > > library("minpack.lm")
> > > > h <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> > > + -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
> > > + 75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
> > > + 6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
> > > + 10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
> > > + 11781.77, 11863.35, 11927.44, 11980.81, 12021.88, 12058.35, 12100.63,
> > > + 12133.57, 12148.89, 12137.09)
> > > > high <- h[1:45]
> > > > MaxFluo <- max(high)
> > > > halfFluo <- MaxFluo/2
> > > > halfCycle = 27
> > > > find_slope <- function(X, Y) {
> > > + Slope <- c(0)
> > > + for (i in 2:length(X)) {
> > > + delta_x <- X[i] - X[i-1]
> > > + delta_y <- Y[i] - Y[i-1]
> > > + Slope[i] <- delta_y/delta_x
> > > + }
> > > + return(Slope)
> > > + }
> > > > slopes <- find_slope(1:45, high)
> > > >
> > > > rutledge <- function(m, s, M, B, x) {
> > > + divisor = 1 + exp(-1* ((x-m)/s) )
> > > + y = (M/divisor) + B
> > > + return(y)
> > > + }
> > > > rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(p$x-p$m)/p$s))) + p$B) - y
> > > >
> > > >
> > > > init = rutledge(halfFluo, slopes, MaxFluo, 0, high)
> > > > points(1:45, init, type="l", col="red")
> > > > estim <- nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B = high[1]),
> > > + fn = rutledge_param, x = 1:45, y = high)
> > > Error in nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B =
> > > high[1]), :
> > > evaluation of fn function returns non-sensible value!
> > > ```
> > >
> > > Where could the error be?
> > >
> > >
> > > --
> > > Best regards,
> > > Luigi
> > >
> > > ______________________________________________
> > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Best regards,
> Luigi
--
Best regards,
Luigi
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