Questions tagged [biostatistics]

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

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18 views

about the microbiome data [on hold]

When we use nonmetric multidimensional scaling for microbiome data using vegan package in R, can we use raw count OTU data? or do we need to perform total sum scaling normalization or cumulative sum ...
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32 views

Creation of contigency table and calculation of effect size (Chi2, Cramer's V)

I am a bit unsure in my approach of applying the Chi2 GOF test to my data and calculating the correct effect size. The situation: I am studying the occurrence of specific biological phenomena in ...
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Is it possible to statistically analyse effect of independent variable on one of two interacting dependent variables?

This is the first question I have posted here so I kindly ask for your patience. My issue is that I'm not sure whether I can apply a statistical test to my experimental data. My research question ...
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14 views

power_transform vs. quantile_transform [closed]

What's the similarities and Dissimilarity of theses two methods that implemented in scikitlearm library?
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15 views

Bias of Pearson correlation estimator of two Bernoulli variables

Crossposting link: https://math.stackexchange.com/questions/3312349/bias-of-pearson-correlation-estimator-of-two-bernoulli-variables Suppose we have two correlated Bernoulli random variables, $X_j$ ...
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1answer
24 views

Analysis of multiple response/check all that apply survey data

I am helping to review a manuscript and suffering from mental block on some data analysis. The data in question is from a cross-sectional survey, a health care provider KAP (knowledge, attitudes, and ...
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10 views

How can I get the sequence logo = C in the first column of the DNA analogy of the book “Machine Learning - A Probabilistic Perspective”

section 2.3.2.1 of book "Machine Learning - A Probabilistic Perspective" uses this Figure to illustrate the application of multinomial models Figure 2.5 (a) Some aligned DNA sequences. (b) The ...
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42 views

How to measure interaction between variables (mutations)?

I have a large dataset of germline genetic mutations from a population of 1,000 individuals both affected and non-affected. I've already looked into individual mutations that are enriched in the ...
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13 views

Comparing means between 3 different groups across time (given that the 3 groups are defined by 2 factors)

I have 3 different experimental groups: 1) Wild-type, control 2) Transgenic, control 3) Transgenic, Drug-treated Therefore, my groups are defined based on two factors: genotype and drug treatment ...
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31 views

What do ellipses of PCA analysis (factoextra) mean?

Biological question: do plants that have been attacked by insects differ in their characteristics from plants that have not been attacked by insects? Data frame includes six numerical variables ...
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8 views

RNA-seq: probabiliy of at least one type I error

I need to find a mathematical expression for the probability of finding at leat one type I error. I know that in general that probabilty is: P=1-(1-a)^m. With a being the probabily of making a type I ...
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Stratified Log Rank Test with Unequally Sized Strata

If I perform a stratified log rank test in a situation with many strata (currently I have 8), in 6 of the 8 there are very small numbers (i.e., 1 or 2%), but the other strata are fairly balanced, how ...
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60 views

How to get confidence intervals for Patient-Years?

In medicine patient-years is a popular concept. Example: $100$ patients are followed for $2$ years. In this case, there are $200$ patient-years in total. If there were $8$ myocardial infarctions in ...
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45 views

Cox regression different results with different combinations of variables

I need help understanding how to use cox hazzard model to calculate risk of death in data from a cohort study. I have a set of data on physical activity and I want to do a cox regression on ...
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1answer
48 views

What is the equation to calculate the sample size for A/B testing? [closed]

I have been searching for information on how to calculate sample size for A/B testing. My research was fruitless. I found many online calculators, but not any blog/paper that explains how the ...
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1answer
19 views

How to find difference between data recorded for 1431 variables for X subjects, across 3 time points?

I am doing research using magnetoencephalography (MEG). I'm performing coherence analysis which, briefly, is a measure of neuronal synchronicity and functional connectivity. For each subject scanned ...
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29 views

Converting annual survival rate to daily mortality probability

In a peer-reviewed paper, I came across the following conversion: Yearly survival rate -> 0.70 The authors have calculated the daily probability of death using (1 - 0.70^(1/365.25)) = 0.000976 ...
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1answer
47 views

How to test whether individual fits to regression line or not

I have a defined regression model for the healthy control (HC) group, with corresponding CIs of coefficients and of E(Y). I would like to test whether individuals belonging to another population (...
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1answer
39 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 ...
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10 views

Chargaff's rule and degrees of freedom of the chisquare

I have a question regarding if and how one should take into account for the extra knowledge that he/she has of a model when determining the degrees of freedom of a distribution, in my case the chi-...
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1answer
49 views

When knowledge of one event tells us nothing about another

I have an example; Say I have two genes on two different locations on two different chromosomes. P(A) = gene is from location 1 P(B) = gene is from location 2 Geneticists believe that knowledge of ...
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1answer
30 views

What type of a test will I perform in R?

I have a dataset which contains data observed for patients who were hospitalized for moderate or severe infection and given one of two antibiotics. The number of days each patient was hospitalized ...
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2answers
126 views

Cox proportional hazard analysis with non-uniform samples; power analysis

We have a study involving 10,000 patients, 5,000 of them treated with drug A and 5,000 with drug B. We want to know if drug A is more effective than B. The median time to event (death) after treatment ...
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1answer
32 views

sample size calculation in 3-arm survival analysis

In a 3-arms clinical trial, with time to event data, either A is superior to C or B is superior to C it will be considered significant. No need to compare A and B. I know how to calculate the sample ...
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40 views

Choosing appropriate statistical tests

I am trying to run stats on medical treatment data and would like your guys and girls help Goal: Comparing two trends of annual percentages for statistical significance. Is one decreasing due to the ...
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1answer
18 views

Batch differences in biochemical measurements - statistical solutions?

I'm working with inflammatory markers from human participants in a current study and have been stumped by between-batch differences. One third of the participants had their inflammatory markers ...
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16 views

How to identify the difference in significance of two different z test for two proportion test?

I have two cell types (A and B) in a tissue. I have 5 replicates of RNA sequencing data in control and treatment condition for cell type and B separately. We are interested in identifying genes which ...
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1answer
88 views

Given two related ratios within a population, derive a third ratio (eg. redheads, non-redheads, and skin cancer)

If People X are N times more likely to have attribute A than non-X People X are P percent of the population then What percentage of A's are X? Example (the numbers are just for illustration). If ...
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1answer
57 views

What test do I use for this? (NOOB biostatistics question)

Suppose I have some subjects and I give each of them a test. I would end up with a dataset like: ...
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29 views

Rank non-normally distributed sets of integers: long read sequencing and phase blocks

I have about 20 arrays of empirical integer values, which are each not normally distributed, with long tails. I am looking for a 'sane and sound' metric on how to sort these distributions, "with ...
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1answer
24 views

Log transformed data

When you log transform data what is being tested on the original scale of the data? And why can we use our log transformed data to answer our scientific question? We are looking at data comparing ...
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33 views

How can I isolate objects from a 3D image volume using normally distributed geometric features

I have '.tif' image stacks that I am analyzing as volumes. For every object, I can get the Volume, surface area:volume, 'sphericity' and Euler number. For every one of those features, the objects I am ...
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18 views

Emergence of Lognormal distribution for the concentration of chemical compounds

I'm currently reviewing the literature about lognormal distributions describing/approximating the variability of a given chemical compound across different cells/ samples etc etc. The main argument ...
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21 views

Statistical testing in clinical research

I just did a univariate binary logistic regression to classify a disease based on some medical parameters. Now only one variable showed significant result (p-value < 0.05). Assuming sufficient ...
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1answer
158 views

How to use Cullen and Frey graphs for downstream statistical analysis? [closed]

How to use Cullen and Frey graphs for downstream statistical analysis? I do not see any difference in normalized and raw data Cullen and Frey plots! Raw data ...
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Model for missing data at baseline?

I am interested in looking at the effects duration of a certain medicine has on an outcome over time assuming the effects to be nonlinear. Some people would have baseline data of before starting ...
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20 views

Environmental variables and management

I have a dataset with 7 forest sites, each with a paired managed and unmanaged stand. In these stands I have 4 - 19 plots where insects have been sampled. Additionally, we also collected a number of ...
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1answer
48 views

Confidence interval for Population Attributable Fraction with several strata

I have used aggregated data to create a table of person-years (pys) and deaths by social class, age and sex. If we consider social class to be a modifiable factor, we can calculate the number of '...
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1answer
44 views

How to report robust anovas (WRS2::t2way and t3way): no df

I have done experiments with a parasitic wasp species, comparing its life table parameters (response variables: longevity (in days), number of offspring and development time of offspring (in days)) ...
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1answer
76 views

Calculating confidence intervals for “excess events”

I have a study that shows 100 deaths occurred in a cohort of high-risk people. Given mortality rates in the general population, you would only expect 70 deaths to occur. The standardised mortality ...
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21 views

Real 1 dimensional non-binary data where Cox Proportional hazards model fails

I am learning about the Cox Proportional Hazards model and understood that it is very flexible, even when the assumption of proportional hazards is not met, e.g. for additive hazards. But say we have ...
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2answers
54 views

Getting ecological statistics right: Learning by yourself

I'm not really asking for reference on ecological statistics (such as here or here), but more on how you can be sure you're doing a new analysis you just learned correctly. I'm often stuck trying to ...
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19 views

What does the decomposition of a relative risk look like?

Say I have a relative risk of smokers that smoked 1-20 cigarettes per day. What is the mathematical identity between that RR, the RR of those that smoked 1-10 cig/day, and RR of those that smoked 11-...
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1answer
28 views

How to make a random draw from a mgcv GAM model

Hi there statistical wizards! I have a (maybe) minor problem, where I would like to use the predicted fit (fit) and standard error (...
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42 views

Model for semicontinuous data with structural and sampling (true and false) zeros

I am dealing with a very hard-to-work data set: fish larval density. It is a semicontinuous data, with 90% of zeros and a right-skewed distribution, with few very large values. One problem is that ...
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12 views

Can ANCOVA be used for the following model

Suppose I have 3 treatment groups, and I have pre- and post-treatment test results. There are also 4 covariates which theoreticlaly can influence the post-outcome. So is it possible to find which ...
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43 views

The difference between the cumulative baseline hazard and the cumulative hazard?

I'm not sure what is the difference between the cumulative baseline hazard and the cumulative hazard? Could you please explain it if you are an expert in this field? Thanks
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58 views

Sample Calculation of Morisita's Overlap Index

I am actually a biologist who has as question regarding how to apply the Morisita's Overlap Index. I have been told to compare two plant species by using this index and 3 other variables for each ...
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1answer
30 views

Risk prediction equation for disease based on concentrations of circulating proteins

I want to derive a risk prediction equation for disease D based on Pa and Pb, where Pa and Pb are concentrations of circulating proteins in the blood. Disease D has two sub types: Da and Db. In Da, ...