Questions tagged [statistics]

The study of the collection, analysis, and interpretation of data.

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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?
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Nei's gene diversity - calculation

I am completely new to biodiversity. I have a question: how do I calculate Nei's gene diversity? The formula I was given is H = 1 – Σpi2 I have an excel file with 3 different loci (Pgi-2, Pgd-2, Pgm-1)...
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1 answer
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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 ...
3 votes
2 answers
130 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) ...
1 vote
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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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1 answer
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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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12 votes
2 answers
961 views

Is it scientifically sound to pool repeated measurements?

I am measuring specific phenolic compounds in leaves of A. thaliana. I have many different varieties, and different treatments. Initially I was measuring one leaf per plant for three plants for each ...
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1 answer
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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
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 ...
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1 answer
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Why does Falconer's formula for broad sense heritability subtract correlation values instead of r^2 values?

Falconer's formula for broad sense heritability is 2*(r_monozygotic - r_dizygotic). Mayhew and Meyer (2017) states: "Subtracting the DZ phenotypic correlation from the MZ phenotypic correlation ...
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1 answer
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How many people need to have the same mutation of a gene in order for that gene to be seen as a feasible candidate for a disease?

I am learning about genome-wide association studies (GWAS) and I know that they are used to see whether certain SNPs are associated with a disease of interest. From everything that I have watched and ...
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2 votes
2 answers
225 views

Definition of semiquantitative

I'd like to understand differences between how biologists and statisticians deal with uncertainty. As a concrete example, I'd like to understand if "semi-quantitative" can be defined in ...
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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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0 answers
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Apply Shannon-Weiner index to evaluate single-cell sample balance?

I would like to identify single-cell clusters where each sample is evenly represented in it. Is it OK to calculate the Shannon-Weiner index from the sample counting data of each cluster? I am worrying ...
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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 ...
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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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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1 answer
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Confusion about how to compute probabilities for linked genes

I am confused about how to compute probabilities for linked genes. The problem that I am solving is this: P generation: AAbbddEEff X aaBBDDeeFF. If A and B are 40 centimorgan apart, what is the ...
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62 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 ...
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1 answer
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Deviation from Hardy Weinberg equilibrium (HWE)

I have a set of 10 genes, each gene contains around 15 SNPs. I have tested the deviation from Hardy Weinberg equilibrium (HWE) for all SNPs. All of the SNPs didn't deviate from HWE, except 5 SNPs in ...
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1 vote
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Using coefficient of variation (CV) for GCaMP6 'synchronised episode' spikes, good idea or not?

Using GCaMP6 we have recorded fluorescence activity of kisspeptin neurons that exhibit synchronised pulsatile firing activity. I measured the intervals between each episode, which are quite variable. ...
3 votes
2 answers
189 views

Is the coronavirus getting less dangerous?

Please note This question is based on data from the UK government's web site (data from the ONS). I am not taking this data as accurate, but am using this as it is the only source of data I can find, ...
3 votes
1 answer
97 views

Probability of all alleles represented in a sample

I'm trying to wrap my head around some formulas presented in the 1992 paper from Chakraborty Sample Size Requirements for Addressing the Population Genetic Issues of Forensic Use of DNA Typing, but I ...
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1 answer
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Why do coronavirus cases graphs have a sinusoidal like shape?

Some screenshots from a canadian website: See this sinusoidal shape? Why is it there? Shouldn't it be a single curve? My main guess is when cases are counted: is it possible that they are counted ...
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: ...
2 votes
0 answers
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Exhalation in human breath, through mouth or nose: which is most usual?

Until now I believed that breath exhalation through the mouth is common for most human beings, and this fact is implicit in several technical contexts of which I can think (sports, music, medical ...
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1 vote
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How to fit simulated with measured data having systematic errors?

Consider a given time series of measured data, i.e. the number of persons tested positive for COVID-19. And consider a simulation - consisting of a model, possibly fed with some parameters estimated a ...
2 votes
1 answer
69 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. ...
-1 votes
1 answer
62 views

Analysing bird diversity data across 2 sites and 2 time periods - Ordinal data. Shannon's and Jaccard?

I am looking for the best way to analyse the data below to measure and compare the bird diversity between 3 sites and across 2 time periods - basically are they different from each other and have they ...
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4 votes
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ABO allele frequencies: Why use the EM algorithm?

In textbooks and lecture notes and slides posted online, determining allele frequencies using blood type information (ABO), under the assumption of Hardy-Weinberg equilibrium, is accomplished using ...
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4 votes
1 answer
264 views

What percentage of individuals infected with COVID-19 don't have symptoms?

There are various statistics estimating mortality of COVID-19 infections, based on how many diagnosed people have died. These numbers are used by various media to extrapolate how many people will die ...
1 vote
1 answer
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Which proteins are part of the most different protein complexes?

Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the ...
1 vote
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Genes and proteins with a significantly inbalanced composition

According to Wikipedia, the median size of a protein-coding gene is 26,288 bp which makes it possible (from statistical considerations) that the nucleotides C, G, A, T appear in roughly equal amounts ...
1 vote
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How many metabolites are in the metabolome of (almost) all eucaryotic cells?

Which small biomolecules (up to the size of amino acids) are present in (almost) every eucaryotic cell and thus part of its biochemical network, constantly and inevitably being produced and ...
1 vote
1 answer
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What is the threshold of significance when measuring difference in proteins' radii of gyration?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess protein compactness. Given two proteins, what difference in radii of gyration can be considered ...
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1 vote
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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
0 answers
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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-...
1 vote
1 answer
124 views

Confusion about read counts distribution in RNA-seq

While reading old DESeq paper (Anders and Huber 2010) I came across following line. If reads were independently sampled from a population with given, fixed fractions of genes, the read counts ...
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1 vote
2 answers
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Why isn't life expectancy normally distributed?

Lots of phenomenon in nature can be plotted onto some sort of normal distribution, and that makes intuitive sense to me (such as human height). Why then, does global human life expectancy drop off so ...
-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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2 votes
2 answers
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What does "genetic correlations" mean as opposed to just correlations?

I'm reading the paper "Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior". In Fig. 4 shows "Genetic correlations of same-sex sexual behavior with various ...
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Mammal Statistics about Natural Death Versus Being Killed?

Is there data determining what percentage of mammals die a natural death (disease, old age) and what percentage die due to being killed and/or eaten by other mammals? In watching wildlife ...
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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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2 votes
1 answer
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Vegetation Monitoring - Why permanent plots

Why do most vegetation monitoring programs rely on permanent plots? Take the context of a single ecological restoration site, for example. Let's say the variable of interest is cover by plant ...
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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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Identifying statistically significant gene rich and gene poor regions

I am just wondering If there any adapted way of Identifying significant gene rich and gene poor regions in each chromosome for a given genome say mm10?
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1 answer
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Proof of mechanisms and causal relationships in biology [closed]

Statistical methods in biology are strongly encouraged: they are quantifiable, unbiased, and usually the only ones that are accepted as evidence. However, it doesn't seem like the whole picture. Say,...
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1 answer
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Where are the statistics for vaccine side effects?

My son told me that that during a discussion at school someone mentioned statistics about side effects of vaccines (I assume that the discussion was about standard vaccines in France). The numbers ...
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1 vote
2 answers
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Is there any relationship between the height of a tree and the number of branches emerging from the main stem?

Is there any relationship between the height of a tree and the number of branches emerging from the main stem? I am particular interested in spruce or fir.