Questions tagged [statistics]
The study of the collection, analysis, and interpretation of data.
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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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1answer
36 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?
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0answers
18 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 ...
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1answer
45 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,...
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1answer
458 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 ...
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2answers
45 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.
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1answer
70 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,...
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1answer
39 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
17 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 ...
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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 ...
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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
32 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 ...
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1answer
38 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 ...
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0answers
43 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
86 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
41 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-...
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1answer
463 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 ...
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1answer
72 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?
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1answer
323 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
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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 ...
2
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1answer
252 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 ...
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0answers
300 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
187 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 ...
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1answer
27 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
64 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
...
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1answer
62 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 ...
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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" ...
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1answer
114 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
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1answer
44 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 ...
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0answers
49 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 ...
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2answers
110 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
72 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
136 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 ...
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0answers
41 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
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1answer
756 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
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1answer
100 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 ...
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1answer
50 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 ...
3
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2answers
924 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 ...
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0answers
246 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 ...
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1answer
364 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
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1answer
104 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 ...
4
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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 ...
1
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1answer
229 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-...
2
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0answers
62 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
418 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 ...
4
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0answers
308 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
103 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
46 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 $R^2$ ...
