Questions tagged [statistics]

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

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20 views

Transfering Odds Ratios to another SNP with high LD?

I have the Odds Ratios (OR) for a particular risk allele in a SNP (I'll call it SNP1). That SNP was unfortunately not genotyped in my data, but I don't want to throw it away. I have looked up the ...
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1answer
439 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 ...
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1answer
110 views

Transcription Factor expression level

Could someone explain me in detail what is meant by "TF expression LEVEL", what does it represent and how is it measured? This is for example used in figure 3 of this paper: A census of human ...
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2answers
2k views

Why Poisson Process for neural firing?

I am new to the world of neuroscience and I would like to understand how come every paper in neuroscience that I read uses a Poisson process to model neural firing. Do I just have a biased sample of ...
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1answer
289 views

How to know what the expected value is? [closed]

I am confused as to how I was meant to know E for a X^2 test in the following question: 2.i and 2.ii give no more information. Not knowing what to do I used E as 0 for the first row and 40 (3+37) ...
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0answers
14 views

Where can I find a list of medical conditions and their incidence rates?

Where can I find a list of diseases and their incidence rates? I'm giving a presentation on Long QT Syndrome, which affects 1 in 2000 people, or 50 per 100,000. I'm trying to find other, more well-...
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0answers
73 views

Flow cytometry analysis

I've performed an experiment wherein I have stimulated cells (cell line) with a drug across different time-points - in its unmodified (Drug) or modified form (H-Drug or M-Drug). All cells are seeded ...
2
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0answers
469 views

What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)

I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in ...
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351 views

Minor Allele Frequency (MAF) higher than 0.5? [closed]

I have a set of data in PLINK format (*.bed, *.bim and *.fam files). There are around 2000 individuals in my dataset. I used PLINK to calculate allele frequencies in the population: ...
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1answer
120 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 ...
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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 $R^2$ ...
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0answers
30 views

Recommendations for an exemplary presentation of statistics related to preclinical drug studies and cellular chemistry?

I am reading Nature's recommendations for collecting and presenting statistics, but would like to also read a few exemplary articles with good charts and data presentation to learn what it looks like ...
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57 views

Is it possible to rank standardized beta coefficients in general linear mixed model? [closed]

I have an experimental treatment at 15 sites and would like to build models to associate usage rates of 4 species with a set of 6 explanatory variables. In the end, I would like to rank the importance ...
2
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1answer
578 views

Asymmetric volcano plot

Nearly all volcano plot I've seen tend to be roughly symmetric around the y-axis, with a fairly equal number of up- and down-regulated genes. What are the potential reasons for a volcano plot that is ...
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1answer
458 views

What is a typical value of the selection coefficient s?

I am trying to gain an understanding of the real world effects of natural selection from the equations, especially comparing it with drift. However I have been unable to find any examples which give ...
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40 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 ...
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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 ...
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1answer
77 views

How correlated are the lengths of tendons in different part of a human body?

How correlated are the lengths of tendons in different part of a human body? E.g., if the we consider two humans, A, and B. Human A has a patellar tendon of length 2 cm, and human B has a patellar ...
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1answer
45 views

Difference in variance of Cys in protein sequences [closed]

Suppose I have got two sets of proteins (amino acid sequences). In one set, I find that the variance in the percentage concentration of the Cys is way more (65.34) than the variance of Cys in the ...
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1answer
198 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 ...
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2answers
496 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
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1answer
382 views

How to get the average number of pairwise differences among populations?

I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of ...
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1answer
66 views

What factors make a sequence evolve non-randomly?

On the wikipedia page about Fay and Wu's H, it talks about a non-randomly evolving sequence may be due to some selection acting or a selective sweep or population expanding/contracting. My questions ...
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1answer
595 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(...
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2answers
129 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 ...
2
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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. ...
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1answer
174 views

Statistical genetics: Allele frequencies that follow a Dirichlet distribution

From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population. We consider a set of $I$ loci and let $K_i$ be ...
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1answer
77 views

Given the number of individuals who have a recessive disorder, how can one calculate the probability that the disorder was inherited? [closed]

Just to be clear, this is not homework. Suppose a biological family has five children, two of whom have a certain recessive genetic disorder that is not sex-linked. The parents themselves do not have ...
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0answers
263 views

How to estimate heritability from breeding data

I have a lot of plant-breeding data (tens of thousands of results) that are composed of phenotypes of parents and offspring. The plants however went trough years of selection and it is not balanced. ...
2
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0answers
73 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 ...
4
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1answer
469 views

How can I calculate Shannon-Wiener diversity index in caves with different kind of habitats and different sampling methods?

I would like to start a monitoring in different caves, compare caves of different age and length, and find out if there are any correlations between these factors and their diversity. I was thinking ...
2
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2answers
735 views

Get Parent GO terms of GO term vector?

I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have ...
4
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2answers
279 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/...
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0answers
58 views

What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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1answer
101 views

Is “aggregate percentage” still a valid term in ecology?

Martin et al. 1946 define "aggregate percentage" as a metric that describes the mean percentage contribution of a group to the total mass/abundance of all samples. The metric is useful in datasets ...
3
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1answer
129 views

Distinguishing Father from Brother

Given the (non-identical) DNA sequences of two men and the knowledge that the second man is either the father, brother, or son of the first man, is the DNA useful in determining which of these three ...
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0answers
447 views

How should one interpret heritability? Is it related to $R^2$?

From Wiki: Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation between individuals on a trait that is due to genetic factors. It ...
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0answers
85 views

Large set of semen microscope images needed

As a course project I have to write an algorithm whose purpose is to analyze a sperm sample (total number, motility etc). In order to do that though, I need to have a sufficient number of images to ...
3
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1answer
141 views

Parametric Bootstrap Capture Recapture

I am using the (one sample) capture recapture for estimating hidden human population. One sample method uses purely frequencies of capture to estimate population. One of my colleague suggested ...
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1answer
195 views

How to statistically test the predictability of evolution? [closed]

Can anyone recommend me an experimental study which tries to test the predictability of evolution? The closest works I found are the studies of fluctuation tests (f.e. classical study of Luria & ...
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3answers
3k views

How statistically significant was the “sweaty T-shirt” experiment?

An Overview of the Experiment. In 1995 there was an experiment that involves young people smelling T-shirts worn by another gender and rating their preference. The researchers found that people ...
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0answers
36 views

What techniques can be used to link environmental conditions to crop yield?

Im interested in how we can determine what are the optimal conditions for crops and how deviations from these optimal conditions affect yield. In the literature I have found two main approaches and I ...
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1answer
464 views

Why perform imputation?

Genetics datasets contain measurements for millions of single nucleotide polymorphisms (SNPs). Some (usually small) percentage of these values are of low confidence, and are labeled as missing values. ...
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3answers
3k views

Do biological phenomena follow Gaussian statistics?

I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
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0answers
30 views

Does anyone use bootstrapping to report mass gain during experiment?

When performing an experiment to report gain of body mass in an experiment, do any of you know of a paper whose authors have used a bootstrap to improve their confidence intervals? I have a n = 10 ...
7
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1answer
688 views

Understanding F-statistics in population genetics

I am reading the classic Weir and Cockerham 1984 paper about $F_{ST}$ estimation. At the beginning (first page, right column), they define 3 statistics. $F$ is the correlation of genes within ...
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0answers
119 views

Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
7
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1answer
26k views

What is the optimum length of abstinence for maximum ejaculation volume in humans?

There have been papers discussing this, and whether the abstinence period should be 1 week, 2 weeks or other [1, 2]. Some think the time to maximum ejaculation volume is even longer than this. doi: ...
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1answer
12k views

How should species density be calculated for a clumped distribution?

Lets imagine 5 plots of different size are sampled for a target species: ...
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1answer
98 views

Independent contrasts with non-homologous traits

I have morphometric measurements for a trait across various animal taxa, and would like to study the relationship between the size of this trait, and the animals' body size. In theory, I can account ...