# modelling 4-parameter curve in R does not match data - how to proceed?

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## 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 ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. model.png (99K) Download Attachment
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## Re: 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 ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 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 <[hidden email]> 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 ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 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 > <[hidden email]> 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 >> > > ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 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 <[hidden email]> 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 > > <[hidden email]> 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 ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.