Questions tagged [statistics]

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

33 questions with no upvoted or accepted answers
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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. ...
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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). ...
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79 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 ...
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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 ...
3
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1answer
197 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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55 views

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-...
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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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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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467 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 ...
2
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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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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 ...
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13 views

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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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 ...
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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 ...
1
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1answer
746 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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220 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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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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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 ...
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259 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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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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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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445 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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84 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 ...
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22 views

How to study the number of herbivores per type of tree and time of day?

Suppose I want to find out the number of herbivores in different kinds of trees, and also compare the numbers between day and night. How would this kind of study be run in practice? It easy to think ...
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0answers
77 views

Cigarette consumption dose-response function WRT health outcomes

I'm curious how health risks (mortality, lifetime probability of cancer, etc) change with cigarette consumption. Specifically, treatring cigarette consumption like a continuous variable, rather than ...
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170 views

“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
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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 ...
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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: ...
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54 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 ...
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34 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 ...
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21 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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340 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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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 ...