# Questions tagged [biostatistics]

The science of statistics applied to the analysis of biological or medical data.

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### What approach would be appropriate for comparing proportions of count data with a small-scale spatial component?

I want to compare the distributions of insects on a plant under different pest control treatments. My data consists of counts of the number of insects per leaf on each plant; the experimental unit is ...
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### 4-arm Olfactometry with odour sources and individual aphids, stat test help for time spent in each zone

I recently completed an experiment looking at 40 individual aphids movement over 20 minutes inside a 4-arm olfactometer with 3 controls (no scent, uninfected aphids, agar) and aphids infected with the ...
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### What tests should I do for this data collected in the field about insects [closed]

I am studying insects at the order level. I have samples from two different plots, A and B. In each plot, samples were taken near the corner and towards the center. I have information about the soil ...
25 views

### How to perform a power analysis for poisson distributed data

I want to perform a simplified power analysis to determine how many cells (samples) to have in control and experimental conditions (assume equal n across conditions). For an alpha level of 0.05, 0.95 ...
22 views

### How to deal with replicates and z-scores?

How would you deal with replicates if you want to calculate z-scores? My ultimate goal is to make a heat map of gene expression. To do so I have to calculate z-scores. The analysis consisted of some ...
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1 vote
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### Rank correlations: what is the difference between spearman coefficient and $R^2$? [closed]

When the data are not normal, how can the Spearman rank coefficient be interpreted differently from $R^2$? As I understand it, when performing a rank correlation, the axes typically shouldn't show the ...
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1 vote
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### Z-scores (heatmap) and statistics with replicates and outliers

My group performed a biological assay.The assay was performed for 6 different cell culture conditions (columns) and for 6 genes (rows). However, it was also performed 5 times (5 replicates) per each ...
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### How to account for multiple measurements of 2 different tissues of a same tree/branch?

I am doing DNA extractions and DNA quality assesment on those results, based on spectrometry (260/280nm values). So i want to compare or see if there is differences between the DNA extracted from ...
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1 vote
52 views

### Are my new intraindividual variability statistics sensical?

UPDATE In response to both of you: First, thank you for your responses. I wanted to clarify things about the threshold and provide some background. The peripheral blood eosinophil count (PBEC) is ...
1 vote
38 views

### How to handle zero-inflated time in Cox proportional hazards model with categorical covariates?

I am using a Cox proportional hazards model to compare the time to an event, adjusting for several categorical variables (X1, X2, and X3). One of these variables, X3, is a three-level categorical ...
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### What methods to use for statistical analysis of a network structure?

I have a network structure (adjacency matrix) and want to find a method that tells me which features of my network are most important to explain my response variable. In this case its an infection ...
12 views

### How to test whether the values in one matrix are significantly smaller than in another matrix?

I have a set of proteins for which I have predicted structures using two distinct methods. For each protein, both methods have generated 5 different structures. My goal is to compare the stability of ...
1 vote
23 views

### Statistically determining a count of particles

I perform experiments to do measurements on various pharmaceuticals. One such measurement is interested in the number of particles which is confined into a small volume. The raw data in my experiment ...
24 views

### Anova not significant but post hoc is - how to interpret?

I have some data on animals, their diet (carnivore, omnivore, herbivore) and the angle of their orbits relative to the skull midline. Typically carnivores have more front facing eyes, whereas ...
22 views

### Sample size for a vector of proportions and simulation

Currently, there are more than 10 variants of omicron virus. Say, variant proportions are X1=0.1, X2=0.35, X3=0.15, etc. I need to calculate the number of samples needed to detect the proportion of ...
29 views

### Post-hoc tests for a Generalized Linear Mixed Effects Model

This question is linked to this one. I wanted to know whether the application of a treatment would have a significant effect on the proportion between healthy leaves and infected leaves. I have the ...
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### My mixed poisson regression shows cross-effects between blocks. How do I report this?

I am analyzing salivary biomarker concentrations from pigs in three blocks. The saliva was taken at three sampling points(variable Time), and I have four treatments. My fixed/main effects are ...
45 views

### estimating category thresholds across a continuous variable using Ordered logistic regression

I've got a set of tomatoes at various stages of ripening, with as an ordered categorical variable ["green","yellow", "orange","red"], along with their weight as ...
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### How to deal with exposure status change and outcome contribution in different exposure status?

I want to estimate the risk of cardiovascular events in patients with diabetes (exposed group) compared to patients without diabetes (unexposed group). How do we deal (in the analysis) with patients ...
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### R - Not sure about nested factor in linear mixed-effect model (lmer)

I am currently studying the presence of biological markers in post-mortem brains of healthy individuals compared to Alzheimer patients. I am not entirely sure I am using the correct design for my ...
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### What is the best way to model the impact of multiple therapies/diagnostic tests on healthcare resource utilization and costs pre- and post-treatment?

I have a methods question that I'm hoping this group might be able to answer. I'm planning an causal inference analysis in R where we want to see how the use of Diagnostic Test 1 rather than ...
1k views

### Why do physicists use sigma while biologists use p values/posterior probabilities?

I work in the analysis of biological data, and am familiar with the use of maths to determine a test statistic, and the comparison of this test statistic with a threshold to evaluate a hypothesis. ...
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### What statistics to use compare many (dependent) ratios

I'm trying to compare the cellular subpopulations of the thymus of transgenic mice. I identify the cells with flow cytometry, and I get results similar to this: Cell type Mouse strain 1 Mouse strain ...
44 views

### Cohen's d effect size of a medication

Studies use Cohen's d effect size to convey the effectiveness of an intervention. As a general rule in psychology, an effect size of 0.2 is considered small, 0.5 is medium, and 0.8 is large. Suppose ...
42 views

### Help with choosing stats test for bird count data

I am a university student working on analyzing some data, and am looking for a little bit of statistics help and guidance. Data overview: I am doing a research project on birds, and am trying to ...
74 views

### How should I be interpreting martingale residuals and zph?

I'm new to survival analysis and am practicing on the AIDS Clinical Trials Group Study 175 Data from the UCI Machine Learning Repository. After using R to fit the Cox PH model, I made a plot to look ...
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1 vote
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### Random permuted block sizes in a randomised clinical trial

What is the best way to choose the block sizes in a randomised clinical trial? Randomisation for an ongoing trial is stratified by site (2 sites) and gender (m/f) for 4 strata - it uses random ...
17 views

### What is the standard deviation/uncertainty of a single observation in a meta-analysis?

I am running a simulation with parameters based on an existing random-effects meta-analysis. I would like to draw individual patients in the treatment group from a normal distribution with µ=the ...
45 views

### Is it possible to perform a three-way ANOVA on non-normal data?

I am not very experienced in statistics so I'm not sure how to tackle this data. I have run an experiment where we recorded the proportion of time some beetles spent in 4 different habitats. Response ...
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### Is it advisable to use PLSR components in another linear equation?

I currently possess biological data from two groups (healthy vs disease) in the form of protein concentrations and I was interested in determining what the relationship was between these protein ...
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### Can Cox or Fine-Gray model include exposure that occurs during observation?

I'm making a Fine-Gray model about pregnancy, but I notice that some pregnancy complications may occur during the observation instead of at the beginning of it because those complications are often ...
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### Is it possible to do a PGLS analysis if some species on the tree appear more than once in the dataset?

I am trying to conduct a PGLS regression on the fidelity and relative size of flies, however some of the species of flies appear in the dataset more than once (their relative size is compared to ...
31 views

### Choosing a sample for a chi-square test of independence

I have about 2000 observations for a dataset I am working on. There are some categorical variables and a dichotomous outcome variable. I am trying to get the predictors. Can I use the entire dataset (...
58 views

### How to calculate pregnant rate

I have two inputs, the ovulation probability for one month, such as A=[0,0,0,0,1,1,6,9,22,25,17,8,4,4,2,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0 ]/100 the pregnancy rate ...
1 vote
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### Determining significant predictors for a dataset with the outcome variable [closed]

I am working on a dataset and trying to get the significant predictors? The dataset contains numeric and categorical variables and there is an outcome variable. What would be the best approach? I am ...
49 views

### How to deal with under-dispersion in negative binomial GLMM?

I have some animal species. I am interested in seeing what is the relationship between the area they occupy (my response variable, p, which is a count of cells) and ...
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### How to convert pairwise dissimilarity matrix into continues predictor in R

I have collected plant species data and AGB from 25 different sites and I want to do regression analysis of Beta-diversity (i.e. dissimilarity among 25 sites) as a predictor and AGB as response ...
32 views

### Propensity Score Matching and Weighted Regression Analysis

I have a dataset of ~N=1000 and I want to estimate the average causal/treatment effect of an exposure on an outcome. I've used propensity score matching to balance baseline covariates, and my matched ...
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### Is GroupKFold needed if some samples have some of their feature values equal?

I am given a dataset $D$ of 10k enzyme-substrate complexes having a lock-key relationship, with each sample (complex) being characterized by enzyme features $x_e$ and substrate features $x_s$. That is,...
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### Please can I have some guidance on analysing policy change on time series data?

Firstly, I am not a statistician, merely a consumer of statistics (NHS Pharmacist). I am undertaking a project looking at the impact of a new clinical test on antibiotic prescribing across multiple ...
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### Measurements necessary for repeated measures model

If I have an repeated measures model for a continuous parameter measured at n visits for each of the p participants in a study how big must p then be to perform the fit? The repeated measures model ...
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1 vote
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### normalizing proliferation percentages

I have a control sample that has one cell type (AP). the control sample has 100 cells total of AP and the 95th percentile proliferation score is 0.5, meaning 95 of AP cells are below this and 5 ...
1 vote
29 views

### What is a good p-value adjustment for a permutational analysis like pairwise PERMANOVA?

I am comparing plant community responses to experimental treatments using the pairwise.permanova function in R. However, there are no clear answers regarding which ...
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### Why or When is between-group variance equal to the covariance among members of a group?

In Introduction to Quantitative Genetics (Falconer) , one of the ways of estimating heritability of a trait is by using a full-sib/half-sib model. In a full-sib/half-sib model, a number of males are ...
1 vote
35 views

### Inference from profile comparisons

What would be a good test to compare patterns of differences among treatments? For example, the Y maze has an outcome of % of entries into each of three arms. Thus, three numbers are generated for ...
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### Working with phytoplankton data - functional diversity

I need help to understand how can I perform an analysis that was suggested by someone else with phytoplankton data. I need to calculate CWM of the community and then, calculate the significance of ...
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### How understand the logic underneath standardization methods?

I have a dataset of very different data and I want to make a multivariate analysis. I am a biology student so I'm very poor in statistics and so I am willing to study this fascinating yet important ...
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### How to test whether the "prevalence ratio" of one marker is higher than that of another

Here is my setup. I have two sets of DNA sequences, one bound by a protein (transcription factor), another not bound by the protein. Let's say I have two candidate motifs, or DNA patterns the protein ...