Questions tagged [biostatistics]

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

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How can I determine statistical significance in seed length and width measurements?

I am researching seed size variation in cereals. I used ImageJ to measure the seeds and generated arbitrary values. Later I converted the measurements to micrometers. I took length and width ...
Eric Whisnant's user avatar
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2 answers
111 views

Hardy-Weinberg Equilibrium Test Result for Merged Genotypes

I was curious if two populations are in Hardy-Weinberg Equilibrium (HWE), and if they are merged, then what happens? To find out, I considered populations from the 1000 genome project data. For ...
statm's user avatar
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Quantifying species detection probability using sign surveys as a function of distance in known occupied sites

I ran a pilot study to determine the probability of detecting a rare African small carnivore using scat (feces) detection dog surveys to assist with future population monitoring and occupancy surveys. ...
Michelle's user avatar
1 vote
1 answer
88 views

Why would GREML in GCTA treat SNP effects as random effects?

I've read many papers, but none of them gave clear answer to my question. For example, https://www.nature.com/articles/s41576-019-0137-z#Sec5 The univariate GREML approach can model multiple random ...
John Smith's user avatar
1 vote
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22 views

MTT assay data pre-processing

I was handed MTT assay data, consisting of drug doses and raw OD scores. The drug treatments were performed three separate times, each followed by MTT assay. I applied some non-linear mixed-level dose-...
Bryan's user avatar
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2 answers
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Methods to obtain the mass distribution of an ensemble of bacteria?

Are there any mainstream methods to obtain the mass distribution of a bacterial population? What kind of assumptions to they make? Could anyone point me to some references?
Gyromagnetic's user avatar
1 vote
1 answer
364 views

When to use fixed effects vs random effects models?

I had previously read some on this topic and my understanding was that a fixed-effect model is when you are sampling an entire population, for example, a school district, a school, or a village. And a ...
neurosciencecalc's user avatar
3 votes
2 answers
189 views

Which statistical test should be used for GC-content comparison?

I'm predicting that certain genes (n=20) are more GC rich than expected in all protein-coding genes. How can I test this hypothesis efficiently? I generated the same number of random genes (also n=20) ...
Lasha Bukhnikashvili's user avatar
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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 ...
Bionoob's user avatar
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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 ...
Galen's user avatar
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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 ...
Galen's user avatar
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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 ...
Galen's user avatar
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34 views

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 ...
Neggor's user avatar
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2 votes
1 answer
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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 ...
EmmaE's user avatar
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1 answer
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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
Nicole's user avatar
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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 ...
ceno980's user avatar
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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 ...
ceno980's user avatar
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2 votes
1 answer
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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 ...
E Tam's user avatar
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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. ...
Roger V.'s user avatar
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1 answer
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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 ...
Lynn Gu's user avatar
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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 ...
ceno980's user avatar
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1 vote
1 answer
263 views

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 ...
John Hon's user avatar
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2 votes
1 answer
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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 ...
Tushar Patel's user avatar
4 votes
1 answer
164 views

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/NMDS) of the beta-...
Roger V.'s user avatar
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1 answer
60 views

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 ...
sonicboom's user avatar
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5 votes
3 answers
205 views

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 ...
JEJS's user avatar
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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 ...
Janey's user avatar
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0 answers
150 views

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 ...
Kayley's user avatar
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7 votes
2 answers
317 views

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,...
Roger V.'s user avatar
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1 vote
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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 ...
Dayne's user avatar
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4 votes
1 answer
173 views

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: ...
Tom Hosker's user avatar
2 votes
1 answer
135 views

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. ...
Winston Campeau's user avatar
6 votes
1 answer
397 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 ...
Hans-Peter Stricker's user avatar
1 vote
0 answers
20 views

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 ...
H_1317's user avatar
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2 votes
0 answers
62 views

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-...
tebiwankenebi's user avatar
-1 votes
1 answer
68 views

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 ...
s33ds's user avatar
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0 votes
1 answer
44 views

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 ...
alex's user avatar
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0 votes
0 answers
64 views

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 ...
user43110's user avatar
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0 votes
1 answer
178 views

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,...
John Toff's user avatar
2 votes
0 answers
34 views

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 ...
Shane P Kelly's user avatar
3 votes
2 answers
270 views

What is the name of this graph/plot?

What is the name of this graph/plot?
DaudAssassin's user avatar
1 vote
0 answers
23 views

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 ...
user491880's user avatar
3 votes
2 answers
97 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 ...
Circus pygargus's user avatar
2 votes
0 answers
38 views

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 ...
Hypnos Stratagem's user avatar
0 votes
1 answer
62 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 ...
megob's user avatar
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2 votes
1 answer
136 views

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 ...
AScientist's user avatar
4 votes
1 answer
75 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 ...
gladys_c_hugh's user avatar
3 votes
0 answers
52 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 ...
Remi.b's user avatar
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6 votes
1 answer
584 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 ...
Ólavur's user avatar
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3 votes
1 answer
58 views

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 ...
bdetweiler's user avatar