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Questions tagged [biostatistics]

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

26
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1answer
2k views

Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
19
votes
3answers
100k views

Deciding between chi square and t test

I am always so confused whether to do a chi square test or a t test in the sums given by my biostats teacher. Does anyone have a simple rule to decide this?
12
votes
1answer
180 views

Biostatistics: Pollen dispersal directionality

What Information am I looking for? Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around ...
10
votes
5answers
10k views

How many (taxonomic) families are there?

Approximately, how many families have been identified? I've often often come across figures for the total number of species on Earth. Recently, I found myself wondering about the encompassing ranks ...
9
votes
1answer
138 views

Is bootstrapping an acceptable way to determine standard error for binding constants? [closed]

I'm measuring binding constants my system and I appreciate the usual methods of using replicates to measure standard errors and using those errors to calculate propagation of error. I'm curious if ...
6
votes
1answer
213 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 ...
5
votes
1answer
356 views

Are descriptive statistics sometimes more useful than tests of significance?

How does the biology community currently feel with regards to publishing descriptive and effect size statistics rather than significance stats? Almost every journal article I read in the cell biology ...
4
votes
2answers
2k 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 ...
4
votes
1answer
84 views

Why genes are assumed to follow multivariate normal?

I wonder why gene expression data are very frequently modeled by multivariate normal distributions. What is the reason for those strong assumptions that the genes follow multivariate gaussian? Are ...
4
votes
1answer
59 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 ...
4
votes
2answers
269 views

Different Effects of Detection Probability Between Presence and Count Data at the Same Location

I'm modeling habitat suitability for a large, mobile animal using occurrence data (presence only - I have no true absence data in this case) collected from camera traps (stations with automatic motion/...
4
votes
1answer
139 views

Is there a correlation between incidence of type 1 diabetes and vitiligo?

Does the data indicate that if you have one, the probability of you having the other is higher than that of someone who doesn't have the one?
4
votes
1answer
137 views

The dominance variance on a single locus

I was reading the book "Genetics and Analysis of Quantitative Traits", by Lynch and Walsh. I how the covariance between two individuals with IBD $\Theta$ gets divided into just the additive variance ...
3
votes
2answers
479 views

On evolution statistics [closed]

This basic evolution theory question has been haunting me since childhood and I'm kind of embarrassed that I can't explain it yet: Consider a butterfly. It's wings have evolved to look like the eyes ...
3
votes
2answers
170 views

What is the name of this graph/plot?

What is the name of this graph/plot?
3
votes
1answer
272 views

What does the Gini index mean in a biochemical context?

What is the meaning of the Gini index, as specificed in this link, which describes the Gini index of beta-glucopyranose bound to hexokinase? Is this true that if Gini index has a very low value that ...
3
votes
2answers
324 views

Choosing appropriate statistical test for ordinal data

Ordinal response variables show up often in biology, but I'm not sure how they are best analysed. Some examples are qualitative assessments (little, many, a lot) or risk assessments (low risk, medium ...
3
votes
2answers
835 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values,...
3
votes
1answer
96 views

Needing help in order to infer the statistical hypothesis tests performed in an old paper

I am in great need of help in order to infer the statistical hypothesis tests performed in an old paper. However I need to make some reasonable guesses only from the abstract of the paper since the ...
3
votes
1answer
42 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 ...
3
votes
0answers
47 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 ...
3
votes
0answers
221 views

Need help to determine the parameters of an experiment [closed]

I need to conduct an experiment where I compare 5 drugs. For the trial I am supposed to use 30 animals subjects. Each drug will be injected to 6 randomly picked animals. After a period of time, 2 ...
3
votes
0answers
274 views

Is there a standard formula/calculation for sexual dimorphism?

Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use $$\frac{\text{Female value}}{\text{Male value}} -1$$ This would give negative values ...
3
votes
1answer
178 views

Niche overlap Index

I wanted to use the compana() function from the adehabitat package in R. I don't really understand the meaning of the data in ...
3
votes
1answer
181 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
54 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
1answer
94 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 ...
2
votes
2answers
437 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 ...
2
votes
2answers
1k views

What is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
2
votes
1answer
51 views

Material on the analysis of (micro)array data

I'm at the moment analyzing cytokine array data. The available material on the statistical analysis of these data is more than unsatisfactory. Since a lot of effort is being made in the analysis of ...
2
votes
2answers
527 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 ...
2
votes
1answer
47 views

H is the set of all possible Diplotypes that are consistent with genotype data

I am new to Biology.SX. I have a statistics background, and have almost zero knowledge in genetics. I am trying to understand some things related to genetics in a certain paper of biostatistics. ...
2
votes
1answer
43 views

When performing mutagenesis for an assay, how do you decide on the sample size of individuals to be mutated such that all genes are covered?

If I want to study, say, gustatory response of salmons to a bile acid, I need to mutagenize a sample of salmon males. However, given that there are many genes involved in this response, what is ...
2
votes
0answers
25 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 ...
2
votes
0answers
33 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 ...
2
votes
0answers
30 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. ...
2
votes
0answers
35 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 ...
2
votes
1answer
575 views

What is the formula to establish ec50 reproducibility with respect to dose response curves for some drug?

The EC50 is determined by fitting a standard curve to the experimentally obtained control values for each dose response curve using some software that does trial and comparison until satisfactory(...
2
votes
0answers
67 views

Estimated protein size using CDs data [closed]

The number of amino acids in a protein is important to predict their size. I used coding DNA sequence (CDs) to predict the average of the protein size of E.coli k12 from a sample provided by the ...
1
vote
2answers
127 views

How to assess if biological measurements follow a normal or a log-normal distribution

I am using a dataset composed by $m$ samples and $n$ features (genes). Each data point is real number. I want to understand how to preprocess data before analysis, in particular: do data points ...
1
vote
1answer
355 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
1answer
392 views

Bootstrap question

I have a question about bootstrapping: The way that I understand it is that each number represents how well a given node is supported. So in the diagram presented, we can see that the "Seal-Bear-Cat" ...
1
vote
1answer
141 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, ...
1
vote
1answer
37 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
109 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
47 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
264 views

Multi-modal distribution for gene expression data

Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly? I'm referring to the expression distribution of a gene across different ...
1
vote
1answer
409 views

Standardized Selection Ratio (SSR)

In this article the athors used the Standardized Selection Ratio (SSR) in order to infer what is the preferred host (anemone) of anemonefish. Here is a quotation coming from their methods: ...
1
vote
0answers
18 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 ...
1
vote
0answers
195 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 ...