Questions tagged [biostatistics]

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

Filter by
Sorted by
Tagged with
2
votes
1answer
30 views

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 ...
2
votes
0answers
17 views

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. ...
1
vote
1answer
58 views

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 ...
1
vote
1answer
51 views

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 ...
1
vote
1answer
32 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 ...
2
votes
1answer
60 views

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 ...
4
votes
1answer
71 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) of the beta-diversity ...
0
votes
1answer
51 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 ...
5
votes
3answers
179 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 ...
0
votes
0answers
57 views

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 ...
0
votes
0answers
42 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 ...
4
votes
2answers
263 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,...
1
vote
0answers
32 views

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 ...
4
votes
1answer
133 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: ...
2
votes
1answer
55 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. ...
6
votes
1answer
301 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 ...
1
vote
0answers
17 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 ...
2
votes
0answers
60 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-...
-1
votes
1answer
62 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 ...
0
votes
1answer
24 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 ...
0
votes
0answers
41 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 ...
0
votes
1answer
160 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,...
2
votes
0answers
32 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 ...
3
votes
2answers
230 views

What is the name of this graph/plot?

What is the name of this graph/plot?
1
vote
0answers
21 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 ...
3
votes
2answers
69 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 ...
2
votes
0answers
35 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 ...
0
votes
1answer
43 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 ...
2
votes
1answer
107 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 ...
4
votes
1answer
63 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 ...
3
votes
0answers
49 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 ...
6
votes
1answer
365 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 ...
3
votes
1answer
45 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 ...
1
vote
0answers
228 views

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 ...
0
votes
1answer
30 views

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 ...
1
vote
0answers
32 views

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. ...
1
vote
0answers
49 views

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 ...
2
votes
2answers
749 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 ...
1
vote
1answer
451 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 ...
1
vote
0answers
310 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: ...
0
votes
1answer
504 views

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 ...
1
vote
0answers
151 views

Biological replicates

We are currently doing an screening where supernatans from a bacteria genus are tested againts a pathogenic bacteria cell culture in a 96-well plate where OD is measured each 2 hours. Each ...
1
vote
1answer
43 views

Query for gene upregulation in cBioPortal

there! Could anyone help me with some biostatistical problems using cBioPortal. We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use ...
1
vote
1answer
134 views

Tools that take a kinship matrix for phylogenetic decorrelation

I have plant genotypes that have been classified as Invasive, Wild or Domestic. I am trying ...
1
vote
1answer
57 views

What is an appropriate measure of determination in genetic studies?

Main Question What is an appropriate measure of determination in genetic studies? I used to think that $R^2$ was such a measure, but I'm no longer so sure. Specifically, it seems that $R^2$ ...
1
vote
1answer
168 views

Is there a gold standard for syphilis?

When you say the Venereal Disease Research Laboratory test (VDRL) has a specificity of x% and sensitivity of y%, what are you comparing to? What is considered as the truth? Because, Wikipedia says, ...
2
votes
0answers
44 views

Calculate signifficance of SNP in specific trinucleotides [closed]

So, I have calculated the frequency of all SNPs (single nucleotide mutations) in some samples and have also found the nucleotides on the 3' and 5' sides of the mutated nucleotide. So I have a list of ...
4
votes
2answers
3k views

What are the odds of being an albino human and have Down syndrome?

I know the odds of a human to be an albino. In Europe and the US it is 1 in 20,000 people (source) and for Down syndrome it is 1 in 1,250 (source). So that means the chance of giving birth to a child ...
3
votes
1answer
268 views

How to interpret Glimmer scores?

I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score. When I look at the documentation, it says about the score, "This is ...
2
votes
2answers
595 views

How do you compare unpaired biological replicates?

I have done proteomics and I have obtained genes with ratios. As an small example you can see my data below ...