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I see MS Excel has several trend-line options; linear, logarithmic, polynomial, exponential, and power functions. What is basis/logic for selecting these functions for biological data? For e.g. I'm interested in understanding the change of abundance either transcripts or proteins vs different time course; my data fitting with polynomial trend-line. how can I compare different samples in this option?

if Excel is not a good option, how can I do this in R? enter image description here

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    $\begingroup$ Is there a theoretical model that would predict this? $\endgroup$
    – Matti P.
    Apr 25, 2018 at 11:19
  • $\begingroup$ E.g. in some applications the "abundance" of transcripts or proteins will be a monotone function of time and fitting exponential curves in such cases may be appropriate. In other cases a periodic behavior is expected (e.g. diurnal patterns) and other models based on periodic functions can be attractive. $\endgroup$
    – hardmath
    Apr 25, 2018 at 11:24
  • $\begingroup$ Hi Matti, No. this is the first time I'm studying this, I could not find any literature related to this. $\endgroup$
    – Kynda
    Apr 25, 2018 at 11:26

2 Answers 2

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This depends on the shape/distribution of your data. See the plot below. The upper left graph depicts a linear relationship, so a linear function suits your data best. The upper right graph, however, is definitely not linear. A linear fit would be bad in this case. Here, we would need an exponential function in order to properly fit the data. Likewise with the polynomial and logarithmic cases (bottom two graphs).

enter image description here

Here's the R-code to create the above graph:

x <- runif(100,1,10)
y <- 3*x +rnorm(100,0,1)
z <- 0.3*exp(x)+rnorm(100,0,1)
a <- 1.1*x^5 - 13*x^4 +8*x^3 -12*x^2 -19*x+1+rnorm(100,0,1)
b <- log(x)+rnorm(100,0,0.05)
par(mfrow=c(2,2))
plot(x,y,main = "Linear Relationship")
plot(x,z,main = "Exponential Relationship")
plot(x,a,main = "Polynomial Relationship")
plot(x,b,main = "Logarithmic Relationship")

In practice you will have gathered data and your task is to model the relationship. First you should plot your data to see how it is distributed. If have decided which fit the appropriate one is, then you can pick one of several functions in R to estimate the models based on the data. For example, lm() can efficiently create linear models.

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  • $\begingroup$ Nice illustrations! Excel can also fit and graph similar data, although the point-and-click interface of the spreadsheet is more difficult to convey in such concise terms. An experienced spreadsheet user should be able to follow the documentation supplied with the software. $\endgroup$
    – hardmath
    Apr 25, 2018 at 11:53
  • $\begingroup$ Thank you @YukiJ , I have plotted the data and see polynomial is the best fitting. What my question to understand is how protein change over the time and what is the difference of change of e.g protein "X" compared to "P". How can I compare this? I'm not very mathy, so no idea what I have to follow. Would appreciate if you have any related study $\endgroup$
    – Kynda
    Apr 25, 2018 at 11:54
  • $\begingroup$ No problem @Kynda . You can also accept an answer by clicking on the symbol left to it, if it helped you. :) $\endgroup$
    – YukiJ
    Apr 25, 2018 at 11:54
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Check out "model selection" or "variable selection". Not sure if it can be automatically performed in excel. What you need is mainly a selection criteria (like AIC, BIC, Mallow's C$_p$, adjusted $R ^2 $ and so on) and perhaps a method to select (Forward, Backward, Stepwise). If you have small amount of models to choose from you can fit all the possible models by using packages like $\texttt{leaps}$ in $\texttt{R}$. Another option is regularization based "selection", i.e., LASSO and elastic net ($\texttt{glmnet}$ in $\texttt{R}$) that is estimation procedures that selects features as a part of the estimation.

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