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Questions tagged [chemometrics]

statistics used in chemistry.

5
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2answers
144 views

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 ...
1
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1answer
25 views

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 ...
0
votes
1answer
90 views

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 ...
2
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2answers
191 views

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
1answer
19 views

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 ...
3
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0answers
49 views

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 ...
2
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0answers
249 views

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 ...
0
votes
1answer
113 views

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 ...
0
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1answer
78 views

Train and test a PLS model with simulated contaminations spectra

The data I have to analyze are as follows. There are three group of samples: the reference samples (REF, 100 samples) and two groups of contaminants (Ca, 100 samples and Cb, 10 samples). I have ...
2
votes
2answers
136 views

Cross Validation with replicates for spectral analysis

I am collecting 20 Mid-IR spectra from 10 samples by taking two measurements for each sample. I want to create a prediction model using PLS. What would be the best way to split the data between ...
1
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1answer
177 views

Summing the abundances of multiple peaks, and comparing the sum to another sample's sum

I think this question may make sense here or in the chemistry exchange, but it is more statistics/chemometrics related so I am hoping you can help! I am working on a metabolomics dataset that ...
0
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2answers
141 views

PLS Regression On 3D Matrix

When doing PLS regression, you normally have a 2D matrix where each row is a sample of known class identity (in the case of a training set) where the 2D matrix is the X, and the class information is ...
1
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0answers
26 views

Mixture models - am I on the right path?

We have 2 chemical parameters measured for material 1 and 2. We are interested in finding out the probability of an unknown sample being the mixture of the two reference materials. Also determination ...
6
votes
1answer
824 views

Mean centering or not in the context of Partial Least Squares

In my current project, I'm using PLS regression on infrared spectra (FTIR). For this I'm using R and the pls function from the plsr package. ...
1
vote
1answer
72 views

Multivariate analysis for a data with different metric units

I have some weird data that I don’t know how to treat them! I have a data of metabolite measurements in different groups of samples with 5 replicate in each group: ...
0
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1answer
60 views

Multivariate analysis approach for multiple classes with varying concentrations?

I am working with surface enhanced Raman spectroscopy to discern the lowest concentration one can see of certain neurotransmitters. Concentrations I use are usually around the nanomolar range. I want ...
0
votes
1answer
268 views

Does addition of intercept term for PLSR and PCR makes any sense?

In principle components regression, we mean center(or standardize) X and using this X we decompose it so that: X = T.P' + E And regression to Y becomes(with ...
1
vote
1answer
277 views

How to know if data are compositional?

I have an environmental data set (LA-ICP-MS), where 46 elements are reported in ppms. I do not know whether my data is a subcompositional (compositional) or not. However, I know that an observation ...
1
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1answer
175 views

PLS prediction if X is centered (using f.e. R package chemometrics)

General question about predictions in PLS, using the chemometrics package in R here for an example. The standard example for <...
3
votes
1answer
994 views

What is maximum likelihood PCA?

There are many papers on this topic, such as this one (pdf). However, I could not find out what exactly maximum likelihood PCA is, how it is applied and for which purpose. Can anyone explain it?
1
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1answer
73 views

What measure should I use to compare two sets of calculations?

Assume I have two sets of calculations produced by two different simulators. There is no way to precisely measure actual values for these calculations, so I'm defaulting to the assumption that one of ...
4
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1answer
61 views

When is it considered a repeated and independent experiment in chemistry?

Sorry for the somewhat confusing title. I was wondering about the use of confidence intervals in the context of chemical and biochemical experiments. The experiments must be repeated and the data have ...
2
votes
1answer
2k views

Prediction of independent data with PLS

In Matlab's plsregress function and in many other statistic toolboxes, there is a BETA vector returned that simplyfies the regression problem to(excluding the ...
3
votes
1answer
157 views

Kruskal-Wallis: how to handle ties that might not be really ties?

I have data from a mass spectrometer that are precise to 6 decimal places and range from 0.1 to 10. However, some items cannot be measured by the mass spectrometer because they are "below the limit of ...
2
votes
0answers
104 views

optim() convergence in fitting gamma distribution to separate peaks of time series data

Trying to fit gamma distribution to each separate peak of time series data (chromatography). As a peak i take local minimum-maximum-minimum part of the data each time. Since the peaks values do not ...
1
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0answers
22 views

Find (latent) variables which correlate with age of samples (Time series correlations)

I have 8 samples of whisky which are all from the same producer, matured in the same type of casks. However, the casks were (naturally) different. My ages range from 5 years to 32 years old, but ...
1
vote
1answer
513 views

Multiple peak fit - decomposing a graph into visible and hidden peaks of the same probability distribution

I have a graph as a set of coordinates (x, y), where x is a progressing time and y is proportional to an amount of molecules (chromatography results). Visible peaks on the graph look like of gamma ...
0
votes
1answer
651 views

Assessing Repeatability of a Multivariate Measurement

I have a measurement that was taken 10 times on a sample. The measurement has roughly 11K points. If you're curious, I'm looking at mass spectrum data. I want to determine the repeatability of the ...
0
votes
1answer
88 views

Is it possible to apply PCA to the reconstructed data of ICA?

I have read that it is not possible to verify the variance and order of independent component extracted from ICA. So, I reconstructed the spectra from matrix A and ST(independent component) then ...
1
vote
1answer
119 views

Overview of multivariate statistics for chemometrics (e.g., Raman spectra)

I am looking for an overview of multivariate statistics for chemometrics. I'm reviewing a number of articles that for the most part are analyzing a large number (300+) of various spectra (IR, UV-Vis, ...
2
votes
1answer
120 views

Linear Regression Prediction Interval for precise y values

When calculating the prediction intervals for a regression function, can the y values be precise values "without errors"? As far as I know, in regression function calculation only the x values are ...
2
votes
1answer
64 views

Is removing points from a calibration rigorous?

When a calibration is generated from a set of standards run on an analytical instrument, should the standards be remade and reanalyzed if not all of the points fit within 20%-30% (depending on ...
1
vote
2answers
111 views

PLS identify only peaks not troughs, and ignore certain region

I recorded a few Raman spectra for varying concentration of a substance. I processed the data in R and these are my steps: Remove baseline using baseline.corr with lambda=1e3 and p=0.01 Run PLSR on (...
1
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1answer
77 views

Can I use Principal Component Regression/Analysis to identify Raman peaks in varying concentrations?

I have data of varying concentrations of a particular substance in water. I recorded its Raman signals between 1 ppt to 1 ppb using identical parameters. I would be using Savitzky-Golay filtering to ...
0
votes
1answer
91 views

Principal component regression loadings show nothing

In my experiment, I diluted a chemical in water and recorded its Raman spectra. Then I repeated this with different concentrations. As I can clearly see some peaks decreasing in intensity when I ...
3
votes
1answer
244 views

How to - regression of a noisy titration curve?

I'd appreciate advice on the correct statistical method to analyse a dataset - Dataset is basically a titration curve consisting of [0.5, 1, 2, 3, 4, 5, 6] pg of starting material and 8 replicates ...
1
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1answer
621 views

Quantifying applicability domain for predictive models?

I have a big dataset and I want to build a classification model (svm, rf, ann etc.). Then I split the original dataset into training set and test set. I build the model using training set. After it ...
1
vote
1answer
25 views

Is it possible prediction of chemical activity with few data?

I have activity data (represented by a real number) for five chemical compounds (and for which I have a set of 600 descriptors) and would like to use neural networks or SVM or any other system that ...
5
votes
1answer
1k views

statistical handling of lab values below limit of quantitation (BLQ)

There were several samples BLQ because of the lower limit of quantitation (LLQ) of the method, e.g. 5 ng/ml or less. Using the statistical program PRISM6 I marked these values together with the ...
0
votes
1answer
200 views

Comparison between fat-matrix

I have two data sets obtained from two different kind of chemical analysis: GC-MS and IR. Both the chemical analysis were performed using the same samples. My aim is to know if there are some ...
3
votes
1answer
1k views

How is “Orthogonal distance” computed?

I was reading the vignette of the R package chemometrics (link). In the second paragraph (right below the first equation) of Page 12, the author writes: the OD (...
0
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0answers
247 views

Optimizing “twenty questions”-like decision tree queries

I'm looking for an algorithm which can optimize the selection of queries used to build a decision tree. However, unlike most decision trees, I am constrained to ask the same set of questions for every ...
4
votes
2answers
1k views

Predicting chemical property (Boiling Point) from a SMILES string

I was trying to develop a model for predicting Boiling Points (BP) given a chemical name. One good and unique (ok, almost) way to encode a name is the SMILES notation string. The details of the ...
2
votes
2answers
125 views

Validate a medical test

I've never done something like this before, thus I do not even know where to start with calculating whatever I need. Following scenario: We measure a medical value (Glucose) with our device, and ...
51
votes
4answers
16k views

How small a quantity should be added to x to avoid taking the log of zero?

I have analysed my data as they are. Now I want to look at my analyses after taking the log of all variables. Many variables contain many zeros. Therefore I add a small quantity to avoid taking the ...