Questions tagged [biostatistics]

The branch of statistics that deals with data relating to living organisms.

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Why is $H_{S}$ divided by $H_{T}$ in Wright's $F_{st}$ equation?

$F_{st} = H_{t}-\frac{H_{s}}{H_{T}}$, where $H_{T}$ stands for expected average heterozygosity in the meta population and $H_{S}$ stands for expected average heterozygosity in the sub-population. As I ...
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Can we infer the orientation of a moose's head from the teeth patterns on tree trunks?

Background I am interested in studying the distribution and patterns of behaviour of moose (Alces alces). Moose chew bark off of the trunks of trees, especially Populus tremuloides. See some of the ...
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Is there a published calibration between footprint measurements to body length in moose?

I am in the early stages of designing a study involving a moose (Alces alces) population. An often-true heuristic is that body parts of an animal monotonically increases in size. There likely exist ...
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How much does dry moose scat weigh and vary in dry weight?

I am in the early stages of designing a study involving a moose (Alces alces) population. One of the important objects of measure are their moose pellets, which I want to take a battery of ...
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Phenotype-to-genotype mapping

My understanding is that GWAS or QTL attemp to extract potential SNP candidates responsible of a particular trait. However, is there any framework that attempts to do the opposite? This is, link the ...
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2 votes
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Temporal space-use modeling - How can I quantify temporal variation into a single value without losing magnitude?

For my ecological research on the impacts of intensity of space-use on vegetation structure I need to quantify temporal variation in the intensity of space-use across years (resulting in a single ...
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How precise does a 1:1 ratio PCR sample mixture (microliters) have to be for the liquid amount ratio to not have any effect on results

Amount of liquid: 5 micro liters master mix 5 micro liters of patient sample
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RNA-Seq: Is it conventional to use a threshold RPKM value to determine if a gene of interest is expressed in a sample?

I am interested in finding out at what stages of development a gene of interest is expressed in the human brain. I am using the Developmental Transcriptome tool from the Allen Brain Atlas to find this ...
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Is there a reference brain sample for the RNA-Seq data in the Developmental Transcriptome tool from the Allen Brain Atlas?

I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain. I have read the official ...
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Why Account for Phylogeny when using Relative Brain Size as a Surragate for Intelligence

This paper tries to relate intelligence, life history, and urban fitness of birds. They use relative brain size of each species as a surrogate measure of intelligence. Although this may not be the ...
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Extrapolating rarefaction curves

I am interested in methods for extrapolating rarefaction curves and/or estimating the true species richness. The ecosystem of interest is the gut microbiome and extrapolation is to higher sequencing. ...
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How many cells are there in C. elegans in each hour of its life?

I'm a high school student planning to write a math essay to model changes in the number of cells in a living organism over time. C. elegans is the only organism that I know with a known number and ...
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1 answer
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Why is it often assumed that biological samples from mice follow the normal distribution?

I am analysing Western blot data. In the experiment, I am looking at the expression level of a certain protein of interest in the brains of wild-type and knockout mice. I have seen online that many ...
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1 answer
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How can the recurrence risk ratio be calculated?

The recurrence risk ratio is calculated as follows: $$ \lambda_s = \frac{\text{risk of sibling}}{\text{risk in population}}$$ where the risk of sibling refers to the risk that a sibling has to get the ...
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What is the best method to check for differential gene expression in large dataset? I want to identify aging differentially expressed genes

My data is RNAseq data and I want to know which all genes (which I am looking for) are differentially expressed with age. I have tried the Kruskal-Wallis test and fold change methods. Do you have any ...
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4 votes
1 answer
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Beta-diversity for data with zeros

Background I am looking into enterotyping the gut microbiome data, obtained by shotgun sequencing. This essentially means performing the Principal Coordinates Analysis (PCoA) of the beta-diversity ...
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Mathematical/statistical models for forecasting population distributions of age, sex, weight, and height [closed]

I come from a mathematical background but I have no experience with the topic of mathematical biology. Are there well established mathematical/statistical models for forecasting the evolution of ...
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3 answers
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Saturated Mutagenesis Screening

I am hoping to mutate the active site of the enzyme I am researching that has 5 residues in proximity with the substrate. I am wondering how many colonies I'll have to assess to theoretically sample ...
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Relationship between BMI and age?

I'm trying to study how age as a confounder may affect the relationship between commute mode and BMI (and design a research proposal). To explain age as a potential confounder, I compared age to ...
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What statistical test would you recommend to compare two animal behavior sampling methods?

I am doing a lab where I am comparing the scanning method and focal animal method. Each method will give me the following: Scanning method: occurrence frequency for each behavior (%), focal animal ...
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6 votes
2 answers
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Long-term efficacy and absence of side effects of anti-covid vaccines

The question is about the methodology/biostatistics of clinical trials (I state this beforehand to avoid accusations of being an anti-vaxxer). As multiple anti-COVID vaccines are offered on the market,...
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Is there a survey on whether people have gained or lost weight as a consequence of lockdown?

I am not sure if this is the right forum for asking such a question. Moderators can of course close it if it isn't and please migrate it to relevant site. Is there a survey/study that statistically ...
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4 votes
1 answer
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Are sizes of potatoes normally distributed?

I'm currently researching the variability of sizes of potatoes when all of the potatoes in question have been harvested from a single field. One question keeps coming up in my statistical analyses: ...
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2 votes
1 answer
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Controlling for phylogenetic signal - what is statistically appropriate?

I am currently collaborating with a fellow PhD student. We are both in the same Biology department, but my collaborator is more of a natural historian, so I am handling the statistical side of things. ...
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6 votes
1 answer
340 views

Statistics: How are protein species distributed over cell types?

There are roughly 10,000 to 20,000 protein species in the human proteome (while I've seen also numbers of 500,000 to 1,000,000). Furthermore, there are roughly 200 different cell types in the human ...
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Correlation seen with low billirubin levels but not the gene that causes Gilbert's syndrome

I was reading the following study on associations between bilirubin and CAD (coronary artery disease). They looked at the bilirubin association, and the genes that cause Gilbert's syndrome, which ...
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2 votes
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Detect differentially expressing cells

I have data (RNA expression values, obtained with in situ hybridization) collected from 1mio human cells. For each cell, I have the expression value of a negative control (non-human RNA) and single-...
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-1 votes
1 answer
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Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
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1 answer
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Easy Hardy Weinberg Equilibrium [duplicate]

Hi My friend and I get 2 different answers to this question. I would like to know how to calculate the value of q. My friend says that 500/1500=q because there are 500 recessive alleles in the ...
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Frequency of nucleotide sequences of specific length in DNA

How frequently would you find the nucleotide sequence GGATATCCGC (5' to 3' direction) by chance in a DNA molecule? On average, how many times do you expect to find a specific 20 nucleotide sequence in ...
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1 answer
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Statistical Analysis for Blood Sugar Measurements

I've conducted a lab aimed towards finding the impact of soluble fiber intake on the change in blood sugar levels. Following an 8 hour fast, I had test subjects consume a fixed amount of carbohydrates,...
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To what extent does the distribution of nerual transmiters in the brain vary human to human?

Suppose $x$ is a position in the brain, and $n_i(x)$ is the density of neuro recepter $i$ around that point. Any given human will have some distribution of neruo recepters $n_i(x)$ through out there ...
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3 votes
2 answers
232 views

What is the name of this graph/plot?

What is the name of this graph/plot?
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1 vote
0 answers
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How many samples to run an association study on B-Cell receptors

We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to ...
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3 votes
2 answers
79 views

Book about ordination in ecology

This is a question I posted on Cross Validated few weeks ago but no response has been given so far. I am looking for a book that would cover a lot of different ordinations techniques (indirect ...
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2 votes
0 answers
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Amount of animals to use for animal trials [closed]

I am working on an independent research project involving animal models. I am unsure how to deterine how many animals (rats) to use for the project. The rats will be injected with different solutions ...
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0 votes
1 answer
52 views

Chart of intra-species genetic diversity across species / phyla?

I am looking for information on how genetic diversity within a species (not between species) differs between taxa. In other words: Is the "spread" in the genetic pool, if measured, for instance, in ...
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2 votes
1 answer
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Why does drinking milk lead to increased fractures?

Milk has always been associated with strong bones due to the high amount of protein and calcium in it. Yet reading it up on wikipedia, A study published in The BMJ that followed more than 45,000 ...
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4 votes
1 answer
67 views

Using proportion or a diversity index when dealing with just two strains

I'm looking at diversity maintenance in an experimental system consisting of just two strains. I have count data. I can calculate their proportions and I can use that data in my statistical models, or ...
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3 votes
0 answers
50 views

How much Open Access Data is there in genetics? [closed]

Type of data of interest I would like to consider Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...) Genetic - phenotype data (disease-related data, QTL, etc...) Sequence ...
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6 votes
1 answer
426 views

Recommendations for textbooks on statistical and quantitative genetics, and genetic epidemiology

I'm looking for a textbook on statistical genetics, quantitative genetics, association mapping, and genetic epidemiology. My interests include, but are not limited to, complex trait analysis, and the ...
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3 votes
1 answer
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Recommended reading to quickly get up to speed on infectious diseases

I am in the beginning stages of a capstone project for my master's in Data Science. For various reasons, I have landed on the subject of Clostridium difficile infection. My background is in Computer ...
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1 vote
0 answers
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How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
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0 votes
1 answer
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Query regarding calculation of survival analysis

According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for ...
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1 vote
0 answers
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Fisher's Method to melt p-values for CpG sites annotated to the same gene?

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
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1 vote
0 answers
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Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
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2 votes
2 answers
835 views

Null hypothesis of Chi-square test for independence

My understanding of null and alternate hypotheses : The null hypothesis is a hypothesis whose plausibility is being tested by a test statstic and is denoted by H0. It assumes that observed data ...
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1 vote
1 answer
454 views

Does one need to perform two Chi-square tests?

A question from my University's Question paper 2016: A newly identified fruitfly mutant, cyclope eye –large and single in the middle of the head is hypothesised to be autosomal dominant. The ...
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1 vote
0 answers
331 views

Using Chi-squared analysis to confirm expected phenotypic ratios of offspring

In a recent question the original poster was faced with deciding which ratios to use in a Chi-squared analysis. They were supposed to decide on, "logically", what test-ratio to use. Example question: ...
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0 votes
1 answer
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Goodness of fit: How to decide which ratio to deal with?

While solving problems of Goodness of fit, I'm faced with an issue, how to decide which ratio to consider to find the test statistic from given set of observations. E.g. 1 A supplied sample ...
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