Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
Oh, I got it! I was sending the fluorescence instead of the cycles x.
Thank you
```
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)
```
On Wed, Mar 17, 2021 at 8:58 PM Duncan Murdoch wrote:
>
> On 17/03/2021 12:37 p.m., Luigi Marongiu wrote:
> > sorry, I don't get it...
>
> Modify your rutledge function to print x, and you'll see the values of
> high printed. x should be 1:45.
>
> Duncan Murdoch
>
> >
> > On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch
> > wrote:
> >>
> >> On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
> >>> yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
> >>> B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
> >>> with? Tx
> >>
> >> No, it's not.
> >>
> >> Duncan Murdoch
> >>
> >>>
> >>> On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
> >>> wrote:
>
> On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> > Hello,
> > I have a dataset from a polymerase chain reaction. I am using the
> > equation given by Rutledge
> > (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> > does not match the data. I ran the same thing in Desmos and instead
> > the profile is correct (attached).
> > Why do I not get the same matching model as in Desmos? I believe the
> > formula in R is the same as the one in Desmos, and I am using the same
> > parameters.
> > Is there a procedure to debug models?
> > Thanks
> >
> > Here is the code:
> > ```
> > high <- 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)
> > plot(1:45, high, type = "l")
> > 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)
> > }
> > desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >max_fluorescence = 11839.8, back_fluorescence
> > = -138.864) , high)
> >
> > points(1:45, desmos, type="l", col="blue")
>
>
> In your calculation of desmos, you are using the Y variable for x in the
> formula. Calculate it this way instead:
>
> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> max_fluorescence = 11839.8,
> back_fluorescence
> = -138.864) , 1:45)
>
> Duncan Murdoch
>
> >>>
> >>>
> >>
> >
> >
>
--
Best regards,
Luigi
__
R-help@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
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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
On 17/03/2021 12:37 p.m., Luigi Marongiu wrote:
sorry, I don't get it...
Modify your rutledge function to print x, and you'll see the values of
high printed. x should be 1:45.
Duncan Murdoch
On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch wrote:
On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx
No, it's not.
Duncan Murdoch
On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
wrote:
On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks
Here is the code:
```
high <- 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)
plot(1:45, high, type = "l")
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)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)
points(1:45, desmos, type="l", col="blue")
In your calculation of desmos, you are using the Y variable for x in the
formula. Calculate it this way instead:
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)
Duncan Murdoch
__
R-help@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.
Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
sorry, I don't get it...
On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch wrote:
>
> On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
> > yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
> > B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
> > with? Tx
>
> No, it's not.
>
> Duncan Murdoch
>
> >
> > On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
> > wrote:
> >>
> >> On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> >>> Hello,
> >>> I have a dataset from a polymerase chain reaction. I am using the
> >>> equation given by Rutledge
> >>> (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> >>> does not match the data. I ran the same thing in Desmos and instead
> >>> the profile is correct (attached).
> >>> Why do I not get the same matching model as in Desmos? I believe the
> >>> formula in R is the same as the one in Desmos, and I am using the same
> >>> parameters.
> >>> Is there a procedure to debug models?
> >>> Thanks
> >>>
> >>> Here is the code:
> >>> ```
> >>> high <- 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)
> >>> plot(1:45, high, type = "l")
> >>> 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)
> >>> }
> >>> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >>> max_fluorescence = 11839.8, back_fluorescence
> >>> = -138.864) , high)
> >>>
> >>> points(1:45, desmos, type="l", col="blue")
> >>
> >>
> >> In your calculation of desmos, you are using the Y variable for x in the
> >> formula. Calculate it this way instead:
> >>
> >> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >> max_fluorescence = 11839.8, back_fluorescence
> >>= -138.864) , 1:45)
> >>
> >> Duncan Murdoch
> >>
> >
> >
>
--
Best regards,
Luigi
__
R-help@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.
Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx
No, it's not.
Duncan Murdoch
On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
wrote:
On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks
Here is the code:
```
high <- 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)
plot(1:45, high, type = "l")
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)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)
points(1:45, desmos, type="l", col="blue")
In your calculation of desmos, you are using the Y variable for x in the
formula. Calculate it this way instead:
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)
Duncan Murdoch
__
R-help@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.
Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx
On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
wrote:
>
> On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> > Hello,
> > I have a dataset from a polymerase chain reaction. I am using the
> > equation given by Rutledge
> > (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> > does not match the data. I ran the same thing in Desmos and instead
> > the profile is correct (attached).
> > Why do I not get the same matching model as in Desmos? I believe the
> > formula in R is the same as the one in Desmos, and I am using the same
> > parameters.
> > Is there a procedure to debug models?
> > Thanks
> >
> > Here is the code:
> > ```
> > high <- 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)
> > plot(1:45, high, type = "l")
> > 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)
> > }
> > desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> > max_fluorescence = 11839.8, back_fluorescence
> > = -138.864) , high)
> >
> > points(1:45, desmos, type="l", col="blue")
>
>
> In your calculation of desmos, you are using the Y variable for x in the
> formula. Calculate it this way instead:
>
> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
>max_fluorescence = 11839.8, back_fluorescence
> = -138.864) , 1:45)
>
> Duncan Murdoch
>
--
Best regards,
Luigi
__
R-help@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.
Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?
On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks
Here is the code:
```
high <- 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)
plot(1:45, high, type = "l")
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)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)
points(1:45, desmos, type="l", col="blue")
In your calculation of desmos, you are using the Y variable for x in the
formula. Calculate it this way instead:
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)
Duncan Murdoch
__
R-help@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.
[R] modelling 4-parameter curve in R does not match data - how to proceed?
Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks
Here is the code:
```
high <- 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)
plot(1:45, high, type = "l")
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)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)
points(1:45, desmos, type="l", col="blue")
```
--
Best regards,
Luigi
__
R-help@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.
