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 <murdoch.dun...@gmail.com> 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 <murdoch.dun...@gmail.com> > > 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 > >>> <murdoch.dun...@gmail.com> 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.