Questions tagged [statistics]
The study of the collection, analysis, and interpretation of data.
152
questions
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1answer
50 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 ...
0
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0answers
29 views
Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers?
I want to compare result from my protein docking experiments to various protein structures of the same protein.
I have two samples and in Sample 1, I have ...
0
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2answers
100 views
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 ...
0
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1answer
52 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 ...
1
vote
1answer
40 views
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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0answers
17 views
Can anything useful be done with stable isotope data for a single species
This is my first biology question.
So I have some stable isotope data on a single species. This data looks similar to the demo data in the siar package for r which looks like this:
...
0
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0answers
53 views
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 ...
0
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1answer
17 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 ...
2
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1answer
29 views
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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0answers
33 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
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1answer
37 views
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?
0
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0answers
20 views
How can I approach this data that has a different total number of results between samples?
I was not sure whether I should post this in Biology Stack Exchange or Math Stack Exchange so I posted it in both.
I was planning on doing a small research for my math class (a final project for the ...
0
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1answer
48 views
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,...
5
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1answer
504 views
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 ...
1
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2answers
49 views
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.
0
votes
1answer
100 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,...
1
vote
1answer
56 views
How to determine the number of parameters in a phylogenetic model?
I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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0answers
20 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 ...
2
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2answers
57 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 ...
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0answers
72 views
Epidemic threshold on a directed network
I am trying to understand the equations used in a paper
(https://www.nature.com/articles/srep00469.pdf)
Mainly I'm trying to understand how the epidemic thershold was calculated using the ...
2
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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 ...
0
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1answer
40 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 ...
3
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0answers
48 views
What is a good approximate functional form for an equation relating plant growth to sunlight?
Question is in the title. I've got daily measurements of daily mean shortwave radiation at the surface, and annual measurements of plant growth (some measure, be it height or biomass or something).
...
2
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1answer
99 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 ...
3
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1answer
50 views
Log-tranformation and GWAS
Before doing any GWAS (genome-wide association study) it is necessary to check for the normality of the phenotypic distribution. If the phenotype is normally distributed only once it is log-...
1
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1answer
714 views
Calculating CV for intra-assay ELISA
Sorry if this is in the wrong thread.
I have to calculate CV for intra-assay ELISA sample OD's. My problem is that i'm finding people are using sample standard deviation in their CV formula, though ...
1
vote
1answer
79 views
Is there a statistical analysis test I can perform that will give me a estimate of total population from my own smaller data sets?
Doing my dissertation on the long term trends in moth populations. I am looking at the trends of specific species. Is there a method to obtain an estimate of total population from smaller samples?
1
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1answer
376 views
Find the length of DNA sequence? [closed]
Given $N=5\times10^3$ and mutation rate is $\mu=10^{-5}$ per site, find the length of a DNA sequence so that the probability of mutation occuring M, is greater or equal than 0.95.
Is there a method ...
3
votes
1answer
43 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 ...
2
votes
1answer
314 views
Book recommendations: biological data analysis/error
I'm working as an undergrad in a tissue culture lab, and I have the most experience with statistics out of everyone in the lab. However, most of the knowledge I have in statistics is from my math ...
0
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0answers
338 views
Distribution of the number of synapses per neuron
There is a mean number of synapses per neuron in the human brain which is not very well known, but is of order 10,000. (Some say, it's about 6,000, other say it's about 50,000.)
What is known about ...
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0answers
217 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
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1answer
29 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 ...
2
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0answers
66 views
Criticism of the significance of fMRI studies [closed]
On the german Wikipedia page on fMRI I read the following
"There is some critisism of the basic assumptions and possible
insights gained from fMRI studies which is based on a constructive
...
0
votes
1answer
72 views
Does pre-operational exercise affect recovery from surgery? Statistical Analysis [closed]
https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210
I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on ...
1
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0answers
40 views
It is correct to construct tree species-based rarefaction curves for birds?
If I register all the species of birds that uses sp1 tree, then, all the species of birds that use sp2 tree, and so on. With this dataset, I can made a rarefaction curve using "number of tree species" ...
8
votes
1answer
115 views
Estimation of species range fragmentation
While discussing species distribution patterns along spatial, temporal or functional gradients one often finds a hump shaped species richness pattern.
This is well documented in many taxa and spatial ...
2
votes
1answer
48 views
How should you choose from the various methods of constrained ordination?
I have a bacterial OTU matrix from various sample points and times. So for each sample I have the sequence counts across the various OTUs that they were assigned to.
I also have a corresponding ...
1
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0answers
53 views
In this poisson distribution in olfactory receptor (OR) pseudogenes neutral mutation rate, how is the mean used?
The 2005 paper A comparison of the human and chimpanzee olfactory receptor gene repertoires describes a poisson distribution, with a mean of 0.701
From that mean, how is the gene disruption rate of ...
1
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2answers
120 views
Mathematics for genetics
What types of mathematics are useful for studying genetics? Of course, statistics is, and I'm guessing set theory and group theory, but anything else? What about ordinary and partial differential ...
3
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0answers
78 views
Should you perform an ordination (such as PCA) of abiotic variables before a Redundancy analysis (RDA)?
I have a dataset of viral 'OTUs' across various sample points from different sites/times.
I also have meta-data collected at these same sample points, for things like temperature and the ...
0
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1answer
166 views
Phylogenetic Independent Contrasts with discrete traits
I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete ...
1
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0answers
49 views
Figuring out an honest indicator in intrasexual selection [closed]
In the first picture, the parameter $r$ seems to compare the direction and strength of two variables. In the second picture, $R^2$ seems to describe the variation of proportion of independent and ...
3
votes
1answer
947 views
Are all phenotypes normally distributed
Reposting from the stats stackexchange.
John Cook, in his blog https://www.johndcook.com/blog/2015/03/09/why-isnt-everything-normally-distributed/, writes that many aren't:
Adult heights follow a ...
6
votes
1answer
101 views
Don't understand figures in this citizen-science mosquito ID project
The Citizen-based mosquito monitoring system is a Citizen-Science vector tracking project that involves using any of a wide variety of cell phones to capture "sound bites" (sorry!) of mosquitos. These ...
1
vote
1answer
62 views
Why does Stereology use Systematic Random Sampling?
I am a student of Neuroscience and in all my textbooks and lecture notes it is written that in Stereology, Systematic random sampling (SRS) is used to obtain sections.
Why it's that and not any other ...
4
votes
2answers
1k views
What's the proper way to determine whether dose response curves +/- another variable (besides dose) are statistically different?
I have an experiment wherein I measured uptake of a certain molecule into cells when delivered using Carrier A vs Carrier B. In other words, for example, I delivered 1, 2, 3, 4, 8, and 10 nmoles of ...
1
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0answers
257 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:
...
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0answers
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 ...
0
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1answer
433 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 ...
