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Questions tagged [biostatistics]

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

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

Example (the numbers are just for illustration). If A redhead is 3 times more likely to get skin cancer than a non-redhead. Redheads are 7% of the population. Then What percentage of skin cancer ...
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1answer
51 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
21 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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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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15 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
44 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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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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Analyzing animal occurrence data to detect a movement bias in R

I have occurrence data for animal locations over several months. These UTM coordinates are coupled with a date and time of occurrence, but they differ from tracking data in that it is not over ...
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1answer
41 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
17 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
35 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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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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1answer
22 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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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
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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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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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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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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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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
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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, ...
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1answer
29 views

Statistical test for change in prognostic score pre-treatment vs. post-treatment

I am working with medical data and specifically determining whether Treatment_X is safe in certain prognostic groups of patients with chronic liver disease. To summarize: a common prognostic score ...
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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 ...
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1answer
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Matching in a case control study

I'm working for a physician who thinks they would like to run a matched case control study, matching on 3 covariates, to assess the effect of exposure to a drug on an outcome. I've never done a case ...
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Stratify phylogeny based on variables - e.g. which ST are represented by high % males

So I have tree file and metadata. Metadata includes sequence type ST (clusters that correspond in most part to the phylogeny), but also some patient data, age, sex etc. I am trying to identify which ...
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Can iterative PCA be applied to grouped data?

My data set consist of 156 individuals with fifteen variables. The variables consist of one body mass (dependent) variable and fourteen (independent) variables of different bird bone dimensions (of ...
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1answer
130 views

Controlling for confounding variables in linear mixed effects models (lmer)

I'm using lmer to test how multiple variables (in this case, treatment, species, and sex) influence avian behaviour. ...
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30 views

Confidence interval from sample quantiles

Context I am running some stochastic simulations in R to determine appropriate sample sizes for a biological problem of interest to me. My method iteratively generates "accumulation" curves which ...
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0answers
19 views

I squared for measuring homogeneity

I can't seem to find a simple resource that explains what I can use the I2 (derived from Cochrane's Q), often used in meta-analyses for, exactly. Most, if not all resources I find on the subject go on ...
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1answer
28 views

Stuck between ANOVA (with transformation) and multinomial logistic regression

I need help in determining the appropriate stat test to use. I want to know if the 5 treatments (including the control variable) has significant differences based on their Antioxidant Activity as ...
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What test should one use when dealing with different treatments in plant clones?

In an experiment involving plant clones there are: 20+ treatments, 5 technical replicates for each treatment (plant clones in which the treatments were tested). Variable of interest is Biomass. Due ...
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1answer
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Simple family medical research

The study involved $20$ families, each of $\sim3$ people. For each patient continious parameter $X$ is measured. Each patient has diagnosis $Y=\{\text{ill},\text{healthy}\}=\{1,0\}$. Problem is to ...
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27 views

Different backgrounds, different similarities with ecospat (R language)

I beg all of you your excuses, because the stupid question. I am exploring niche conservatism in five species of Ericaceae. I created two backgrounds sets in order to explore niche similarity (using R ...
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1answer
70 views

Genomics Stats Problem

I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding. I have identified 728 sequences of interest. 597 of these ...
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biological basis for excluding values outside 3 standard deviations from the mean? [duplicate]

Is there any biological basis for excluding outliers in a dataset of blood cytokine levels (e.g. values outside 3 standard deviations from the mean for each cytokine) as measured by multiplex ...
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Model for hormone levels over tissue cells

I have a certain type of biological data and I am unsure about how to model it. The data represent the amount of 3 hormones detected along 20 consecutive cells of a certain plant tissue. I think there ...
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1answer
48 views

R code glmer: Different results with same data

I'm trying to run a mixed model analysis and so far I've found two ways to write a negative binomial distribution model for my data: ...
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1answer
65 views

Correcting data using poisson-regression

I'm new to stats and I was wondering if anyone had any good resources that could explain to me: How one can correct their data (false-positives) using Poisson-regression. I've been looking for some ...
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55 views

Warnings using glmer() in R

I'm trying to analyze the differences in the number of plant species found in different types of fields. The number of species per sample is a non-integer because I had to adjust the number to account ...
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test on fold change of the mean vs. mean of fold changes [duplicate]

Suppose we have 5 subjects. For each subject, biomarker is measured at t0, t1 and t2. Measured values are skewed. We want to compare the values at t1 and t2. When we have skewed data, usually we do ...
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Is there a method that's better than clustermaps for clustering samples which have a n of variables but only two possible outcomes?

For each variable there are two possible outcomes 1 or 0 (True or False): It shows the appearance of particular species on different localities. Mine goal is to cluster/classify similar localities ...
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2answers
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Odds ratio? Can someone help me with what these stats from a paper mean?

this paper I'm reading is on MAOA and violent offenders. From what I understand, an odds ratio of 1.71 means that the violent offenders were almost 2x likely to exhibit the low activity MAOA compared ...
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About standard deviation expansion

Recently, I read an academic paper. There was a formula that I could't understand. SD represents standard deviation, n (n+1) represents the number of samples. Does anyone know how this formula is ...
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1answer
101 views

Proof that random assignment guarantees the same probability for the individual to be selected?

Consider a completely randomized design, where every unit is randomly assigned to a treatment group. Let's say we have 30 observations and 3 treatment groups. When we choose one observation at random, ...
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Difference in library size in next-generation sequencing and differential expression analysis

A common observation in the next-generation sequencing experiments (eg. RNA-Seq) is the difference in the total number of uniquely aligned reads between experimental conditions that we want to compare....