Questions tagged [chemometrics]

statistics used in chemistry.

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How to compare results to a reference with multiple measurements

I have run a pilot test in the laboratory to see which method is best out of 5 different ones. I have reference numbers for a range of measurements to compare these against and then my results for the ...
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How to make a Ramanmetrix model accept values other than the Raman spectra for input? [closed]

I am working on a project to automatically evaluate Raman spectra from a production process. It already works for some compounds with the chemometrics software Ramanmetrix (desktop version 0.5.0). ...
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Non-Linear data fitting for kinetic data

I am trying to fit a two_site model which I derived, (basically, rate as a function of pressures of reactants and products) to my experimental data. Just want to check if the logic below is fine, ...
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Estimating the most abundant isotopomer of an isotopic distribution

i'm trying to pre-estimate the most abundant isotopomers of isotopic distributions. as a simplified example, picture a molecule with an increasing number of carbons the natural abundance of carbon's 2 ...
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The standard error of precision from the standard error of intermediate precision and repeatability of a analytical chemical method

A validation report of an analytical method (to determine the assay of a product) is given and the goal is to try to determinate the overall uncertainty of it. I started with calculating the standard ...
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Reporting post-hoc test with letters (two way anova)

i am testing soil chemistry in soil that has been samples in fields subjected grazing. So two levels ( grazing treatment and soil depth). I have used a two-way ANOVA after testing for normalisation ...
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How can Mass Spectrometry have high sensitivity but average reproducibility?

I am reading up on mass spec from this link: https://www.ebi.ac.uk/training/online/courses/metabolomics-introduction/designing-a-metabolomics-study/comparison-of-nmr-and-ms/ They state: The two most ...
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Comparing two independent variables (one numeric, one categorical) against one categorical independent variable? ag

Sorry if this question is a repeat. I'm new to R, and writing up a chemistry-focused meta-analysis (in collaboration with a statistician, but they're on holiday until November). I have three variables ...
Snippens's user avatar
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Reconstruct IR Spectra Based on PLS Model

I am currently using the scikit-learn package in python to setup PLS models (sklearn.cross_decomposition.PLSRegression) to predict the concentration of different substances based on IR spectra. In ...
PotatoOwl's user avatar
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Is it valid to change the classification criteria of a model after it's been created?

(Please note, I'm a chemist with some minor experience with ML, nothing formal) I am reading this paper that is using a DNN to predict (via classification) if a certain molecule has a good score when ...
DK_chemistry's user avatar
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Difference between the terms "Frequency" and "Abundance"

How does Abundance or Relative abundance (Chemistry) differs from statistical frequency? Or it is just another term for statistical frequency in context of chemistry? Update: here are some example ...
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What is the distribution of the pKa from the Henderson-Hasselbalch equation given log-normal concentrations?

Background The Henderson-Hasselbalch equation is given by $$\text{pH} = \text{pK}_{\text{a}} + \log_{10} \left( \frac{[\text{Base}]}{[\text{Acid}]} \right)$$ where $\text{pH} = -\log [\text{H}^+]$. ...
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Question about confidence interval and standard errors on graphs

So I made a graph in R, it’s a linear regression of the same sample at different concentrations. It has a confidence interval built into it of 95%. Then I had to determine the concentration of an ...
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How can I use the trend of a graph to plot the next point?

I created a hypothesis for a chemistry assignment and then conducted an experiment. The experiment resulted in a graph that had a downward trajectory. It looked like this: I found the data points by ...
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Graph Classification via Random Forest

This is my first post here, just a brief presentation: my name is Gianmarco, I’m Medicinal Chemistry undergraduate student who is preparing his dissertation, my idea would be to create a classifier ...
Gianmarco Luchetti 's user avatar
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Using compositional data analysis to represent chemical compounds

I've recently got some insights about compositional data analysis, wondering whether it could be suitable for the framework I'm currently in. Recently, I've been very interested in trying to find some ...
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Fitting sums of Gaussian-like density functions

I acknowledge that similar question has been asked a couple years ago, yet it still seems unresolved. Ignoring the domain knowledge, the statistical problem behind is to fit a non-linear regression ...
drosophilaxx's user avatar
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Unlabelled spectral data: use PCA to find distint spectra

I have many (Raman) spectra which are unlabelled. I would like to use PCA to distinguish them, i.e. say all these spectra are of type A, these other spectra are of type B... etc... Does this make ...
randomwalker's user avatar
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Should I use the prediction interval or inverse prediction interval to calculate the uncertainty of $x$ when using reverse regression?

I'm calibrating a piece of lab instrumentation. I create solutions of known concentration ($x$) and measure my instrument response ($y$). On unknown samples, I measure the response and use the ...
Kevin Nowaczyk's user avatar
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How to choose priors for experimental data

My question results from the subjectivity of priors, and if there are bodies of work that help to create a more objective approach towards prior choices. My question specifically is to do in the realm ...
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How to test if a river affect another?

I have two rivers, two monitoring stations placed in each river, and two datasets. One river is a tributary of the other. The datasets are complete, pH, metals, field parameters (flow, temperature, ...
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Model Architectures for functional graph or data series type data regression problems using PyTorch, FastAi or TensorFlow

For a university assignment, I am currently trying to build an optical sensor to supervise chemical reactions in pipes. Two sensors are installed in the pipe, around 1mm apart from each other, and ...
passwortknacker's user avatar
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Multiple Linear Regression with more variables than samples

I'm currently learning chemometrics for my work and I have a simple question about Multiple Linear Regression (MLR). Just to explain the context: I am simply using UV-Vis-NIR spectra (2500 wavelengths)...
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Factors given by DoE can experimentally not be reached

We are running a DoE in a CCD manner at the moment. One factor is quite difficult to reach and to reproduce: Humidity because it has to be set by chemical reactions. To be more concise: The factor 56 %...
Ben's user avatar
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Determining whether new data is "in distribution" with training data

I'm hoping to use machine learning to predict chemical properties of various molecules. Many chemistry machine learning research papers that I come across talk about model generalizability issues ...
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How to determine statistical significance of one independent variable by two dependent variables?

(I originally asked a syntax question on stackoverflow here, but in addition to an answer I was told my statistics method itself wasn't great - so now I'm here!) Without getting too into it, we did ...
Mulligan's user avatar
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How do I record randomly assigned data succinctly in a table

Please forgive me if I am posting this in the wrong forum. Here is the context of my question: I am conducting a drug trial, of sorts. I have 7-8 potential candidates for the treatment. Between ...
Rushi's user avatar
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FTIR quantitative methods to analyse / quantify changes in chemical bonds using R / Matlab

What quantitative method could I use to detect whether the radiation of sample significantly affect the chemical bond? Spectra is measured for radiated and non radiated chemical bonds and within ...
user's user avatar
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Clustering data based on correlation

I have a dataset where each row represents a sample and each sample is described by its chemical composition. You can see the 10 first rows of the dataset in figure 1. Figure 1 - Each row represent a ...
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Chemical Analyses

We have two groups of chemical sample results reporting the concentration of a dissolved substance. If I want to compare the two groups I can just carry out a simple t-test. This will say whether ...
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How to calculate risk ratio for chemical substances

Simple example: Three different chemical substances are given to patients (each to 5 patients). Some patients die, some not. Samples (number of patients) are not equal. How to calculate the rate of ...
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Suggestion for a statistical test

I hope this is the right forum for chemometrics related questions well. Imagine that we have a list of tabulated molecular properties for 40 different molecules such as A) dipole moments B) water ...
AChem's user avatar
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Interpolation versus imputation for time series on chemical profiles of water wells

So I am working with some data on water wells and time series of chemical pollutant tests on those wells. There are 10 chemicals and 10 years in the data. My goal is to do some clustering on the wells ...
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Function to fit acid reaction curve

Data in the image below shows a variable DME reacting to the increase in acid concentration. It looks like it has a very fast increase from when the concentration is raised from 0 to 0.5 and then a ...
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Which statistical test should I use, t-test or another one?

I want to compare two samples. Each of them was dried by two different methods, and I studied their physicochemical characteristics (pH, titratable acidity, total sugars, etc.) to see the influence of ...
fati shaun's user avatar
2 votes
1 answer
367 views

Is this an example of where I shouldn't scale before doing PCA / PLS?

I'm working with NMR spectra (it's a common chemical test). There are various peaks of the signal across a range of ppm values. I'm trying to relate the NMR spectra of various samples to a ...
Arthur's user avatar
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How to estimate the uncertainty of a function that has to be solved numerically

Consider I have a function: $PV_m^3 - PbV_m^2 +aV_m+ab=RT$ In this example I have measured the uncertainties in $P$ and $T$ experimentally and the errors in $a$ and $b$ can be assumed to be zero. ...
tionichm's user avatar
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can the parameters of this nonlinear equation be reliably estimated using a limited set of experimental data?

A chemical system at equilibrium is described by this equation: $$ D_{tot} = D + D \cdot \frac {P \cdot X}{D+K_P} + D \cdot \frac {E}{D+K_E} $$ The only parameters that the experimenter can control (...
user6376297's user avatar
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Adjacency matrix of amino-acid residue [closed]

How to get the mathematical representation of the chemical bonds in protein residue or the whole protein? Is it possible to get the connectivity matrix or a pairwise description? The example in the ...
Pol Bel's user avatar
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7 votes
2 answers
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Exclude observations with measurements below limit of detection?

I am analysing a dataset for the relationship between an exposure variable x and a response y (in my case, these are urinary ...
Gux's user avatar
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Reporting model uncertinty

I hope I'm using the right terms here. I've generated a statistical model (PLS regression) based on LWIR (8-10.5 micrometer) spectrum from some lab samples. This model predicts the concentration of a ...
user88484's user avatar
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Can one use parametric regression tests (e.g., Pearson's R2) on summary statistics (that are normal) derived from non-normal data?

Can one use parametric linear regression tests (e.g., Pearson's R2) on summary statistics (e.g., mean and median) that are normal but derived from non-normal data? I am specifically dealing with mean ...
Sid Roy's user avatar
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Build a statistical model based on small sample size

I hope my question is not too wide and that this is the right place to ask it. I'm working in the field of spectroscopy and chemometrics. I'm building a statistical model to predict pollution levels ...
user88484's user avatar
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3 votes
2 answers
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Intersections of chemistry and statistics

I am asking this question for a friend who knows a lot of chemistry and is now studying statistics, primarily since he heard this is the age of data and one should know statistics. However, he is ...
1 vote
1 answer
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Matching of graph peaks over time

I am a programmer but my data analyses/statics skills are non-existent. I am a quick learner though and no problem I have set to solve has yet to become unattainable (let's hope this is not the first ...
Afonso's user avatar
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inverse.predict chemcal package

I have noticed that the inverse.predict function (chemCal package) does not take into account all the degrees of freedom of the ...
AnnaB's user avatar
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Calibration Curve v. Linear Dynamic Range [closed]

We have a piece of analytical chemistry equipment (a mass spectrometer for those who care), that has the capacity to generate a "Response value" (Area under the curve) that correlates to the amount of ...
Ethan's user avatar
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2 votes
1 answer
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How to determine when a chemical steady state procees has been achieved?

I'm trying to figure out what statistical test to use to determine when a chemical process has reached steady state for temperature and the process for a process tool. For example I have a process ...
Rob's user avatar
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3 votes
1 answer
191 views

Dimensions of clustering results

My PhD research (computational organic chemistry) often generates large data sets (>10000 entires) of 'conformers' - where a conformer is basically the spatial arrangement of atoms in space. From ...
James's user avatar
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Testing principal component analysis residuals between groups

I have built a calibration model using principal component regression relating PCs extracted from multivariate spectra to their calibration factors. We are trying to determine if our calibration model ...
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