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Questions tagged [biostatistics]

The science of statistics applied to the analysis of biological or medical data.

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Correlation of binary variables

The presence of 15 different types of bacteria was analysed in a sample of 250 people in a cross-sectional study. They were coded as binary variable (1=present or 2=not present). I need to find out ...
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Examples of striking/pedagogic large dataset analysis in biology [closed]

This question belongs in "Cross-Validated" as well as "Biology" I am looking for example datasets that I could use both for teaching and for my personal training, that would be good examples of very ...
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test on fold change of the mean vs. mean of fold changes [duplicate]

Suppose we have 5 subjects. For each subject, biomarker is measured at t0, t1 and t2. Measured values are skewed. We want to compare the values at t1 and t2. When we have skewed data, usually we do ...
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Is there a method that's better than clustermaps for clustering samples which have a n of variables but only two possible outcomes?

For each variable there are two possible outcomes 1 or 0 (True or False): It shows the appearance of particular species on different localities. Mine goal is to cluster/classify similar localities ...
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Is it possible to use Multivariate regression analysis in the below mentioned research?

In a study we want to evaluate relationship between many varibles with a disease; for example gender(male/female), age(quantitative), weight(quantitative), dibetes(yes/no) etc... Most of our ...
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2answers
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Odds ratio? Can someone help me with what these stats from a paper mean?

this paper I'm reading is on MAOA and violent offenders. From what I understand, an odds ratio of 1.71 means that the violent offenders were almost 2x likely to exhibit the low activity MAOA compared ...
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19 views

About standard deviation expansion

Recently, I read an academic paper. There was a formula that I could't understand. SD represents standard deviation, n (n+1) represents the number of samples. Does anyone know how this formula is ...
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1answer
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Proof that random assignment guarantees the same probability for the individual to be selected?

Consider a completely randomized design, where every unit is randomly assigned to a treatment group. Let's say we have 30 observations and 3 treatment groups. When we choose one observation at random, ...
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12 views

Difference in library size in next-generation sequencing and differential expression analysis

A common observation in the next-generation sequencing experiments (eg. RNA-Seq) is the difference in the total number of uniquely aligned reads between experimental conditions that we want to compare....
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30 views

How to Normalize Counts Correctly?

I am not sure what is this type of problem called, so a ref would do wonders. I am calculating the heritability of diseases among a population. Here is the catch: the age distribution of diagnosis ...
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What test should I use to test enrichment of domains in mutation set?

I have a list of mutations from a certain disease with affected proteins listed. Proteins have multiple domains, and I'm interested which domains are overrepresented. Example values: Humans have ...
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1answer
27 views

What hypothesis test to use for partially paired non-normal data

I have two groups control and test. For both groups data was collected at two time points : One is Baseline and other End of Study. Data is not normally distributed. However, only 50% of data is ...
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1answer
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qPCR Gene expression validation and multiple testing

It's common practice to adjust for multiple testing when analyzing high-throughput gene expression data, eg. RNA-seq and microarrays. Despite this, researchers routinely select a subset of genes for ...
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significance test by confidence interval in complete randomization design(CRD)

In page 91 of this book, Design and analysis of experiments by Montgomery , the author stated after Equation (3.30) that: Clearly, if the confidence interval in Equation 3.30 includes zero, ...
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1answer
26 views

what is x per 100 person years mean?

In medical papers, it is very common to calculate incidence rate and mention it's unit as per 100 person years. What does this means? I know that incidence rate is the amount of people got the event ...
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36 views

Can I calculate Pearson's correlation coefficient, $r$, for variables with categorical and numerical values?

I have been reading a paper and I have found a table that felt very strange for me. The researchers have calculated $r$ value and related it to a categorical factor. From my knowledge $r$ is a ...
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Randomly select three groups with equal means

I am looking for a method which I can randomly select 100 subjects from each of 3 populations so that each selected group has equal mean body weights. The population data I will be selecting from will ...
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14 views

Results from BRTs and GAMMs differ

I have recently run some biological density data through a boosted regression trees (BRTs) and a generalised additive mixed-effects model (GAMM) to find the best environmental predictor of long-term ...
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Which statistical test to use in R? Unbalanced design with one dependent variable and multiple independent variables

it's been a while since I've had to do any statistics and I need a little help determining which statistical model/test to use in R. My background is more with multivariate stats, so it's been a while ...
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1answer
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Baseline values unequal across two treatments in a repeated measures design. A question about controlling for baseline values in lme

I have data on a repeated measures study with measurements on various outcomes taken at 0,6 and 12 weeks. An issue I have run into is that baseline values for various outcomes are not similar between ...
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2answers
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Can I have a categorical variable (similar to the likert scale) on the predictor side of the equation in lme?

My mixed model looks something like this weight ~ age + sex + fruits + (subject | time) The predictor fruit has been converted to a categorical scale of High ...
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1answer
32 views

Test whether the variance in one group is higher than In another

I have 63 groups of microbes that elicit a specific reaction of the immune system (cell frequency). In each group, there are 3-10 replicates and I want to check in which groups the variance is ...
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26 views

For my data, should I use a Kruskal Wallis or one-way ANOVA test?

I read through some literature online and did some investigating on my data and the type of scales my data represents. In my data set, I have my independent variable called ASA status (this is a ...
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1answer
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Antisense Transcript Level

The basic biology says genes on the DNA, get transcribed to mRNA (sense transcription), and the RNA will be translated to proteins. but sometimes, a gene can have transcription from the opposite ...
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What role(s) does Statistical Computing / Computational Statistics play in Clinical Trials?

I am going to pursue a PhD in Statistics, and the two fields that I am really interested are Statistical Computing / Computational Statistics and Clinical Trials (mainly because I like doing ...
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1answer
36 views

Standard Error of the ratio of multinomial and negative binomial variables

What is the correct way to compute a standard error of the ratio between random variables following multinomial and negative binomial distribution? I asked a question about computing variance in the ...
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1answer
26 views

Estimation of partitioning error in next-generation sequencing experiments

[Edited: explanation of the partitioning error] I would like to estimate how the initial number of molecules (or the level of gene expression) affects reproducibility between technical replicates of ...
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How do I know the margin of error of my predicted values?

Questions will be written using bold formatting: I have come up with a model on R that gave me the following output: I've been asked to create a confusion matrix in order to compare my predicted ...
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How to test null hypothesis of “observer A sights animal at the same time that observer B sights animal”

I have 2 observers at different platforms making sightings of animals in the wild. Observers work independently of one another. Observers record when an animal was sighted, as well as the location of ...
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Analyzing Pre/Post Binary Outcomes - What type of model is appropriate?

I apologize for the rudimentary questions. This was not my study, and I am only tasked with analyzing the data. Background I am analyzing data on awareness of tobacco health risks before and after an ...
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1answer
27 views

Difference between log normal probability density values

just reviewing two resources, I noticed a difference between the log normal p.d values : One is here which takes the e to the power in which it contains ln(x) the other is here Which on page 5 , ...
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29 views

Writing syntax for bivariate survival censored data to fit copula models in R

Am required to fit copula models in R for different copula classes particulary the Gaussian, FGM,Pluckett and possibly Frank (if i still have time). The data am using is Diabete data available in R ...
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1answer
75 views

What statistical tests should I use on my data?

My project is on the behavioural responses of anemonefish to a camera flash at different depths. I only had two weeks and no internet to collect my data, please don't judge me too hard! My ...
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2answers
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Terminology for 'prevalence' when it's number of people and not a proportion?

'Prevalence' is usually used to describe a proportion or rate, e.g. '5% $\pm$ 2% of the population are Blue'. What do you call this when you estimate the actual number of people in a population with a ...
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1answer
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How to calculate correlation of 2 variables combined

I have data on 2 histone marks that influence chromatin density. I have calculated individual correlation scores using the cor.test() function in R for both. I would like to combine the 2 together to ...
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1answer
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Why are PhD programs in statistics coursework heavy relative to PhD programs in the basic sciences?

This might go better on academia stack exchange, but it seems probably the people who know the answer are on cross validated.. This is a pattern across the US. My classmates in, e.g., neuroscience ...
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1answer
43 views

Difference between NA and None in biological dataset

I have collected environmental data on animals, and am seeking help on how to deal with certain variables where a non-numeric value is informative, but also problematic. I have three variables that ...
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30 views

Test distribution normality from grouped data in R

So, there is the question: is there any statistical methods exist to apply normality test (hypotesis check) for grouped data? For example, take a look at data frame: ...
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2answers
33 views

Best statistical test to compare proportions of count data

I have taken photos of 30 animals moving around an arena. The arena has 4 different configurations, and I have 500 photos for each animal in each type of arena (taken throughout the day). I have gone ...
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1answer
58 views

multgee for repeated measure multinomial regression

I am trying to analize my experiment results according to the multgee reference pdf, but I have some warning message. My dependent variable is a 5 level categorical variable. I have 12 eyes of 6 rat,...
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1answer
159 views

Biological and technical replicates - mixed model?

I'm trying to make sure I use the correct statistical tests on a group of experiments. Suppose I perform 5 experiments. In each experiment a single batch of cells is partitioned into 6 batches of ...
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1answer
29 views

Statistical test for differences between proportions, with many zeroes

I have collected data in the form of percentages, ie. what % of the population has Trait A? I measured the frequency three times for each population, giving three replicates. My ultimate goal is to ...
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1answer
53 views

Deep learning in medicine(Articles)

I am looking for the articles in Medicine, where deep learning techniques were applied. I googled but I found only tutorials. Maybe you can provide me good articles?
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What statistical test would be best for before and after comparisons of multiple similar groups?

I can't exactly give the problem I'm working on but I will give a sensible example of how it looks: I have 4 groups of people: diabetes, depression, schizophrenia, dementia, notice how a person with ...
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109 views

Correcting for noise in gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a logistic regression classifier. I also ...
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101 views

Does the absolute values of the %IncMSE in Random Forest hint at predictive power of a variable?

I am new to machine learning. I am researching the drivers of plant species richness in woodlands. I have the species richness and a set of predictors, eg, pH, soil organic matter etc for around 100 ...
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35 views

Can populations of different sizes be compared sensibly?

I am new here but have a question about population comparisons. I am trying counting pollen grains using an Scanning Electronic Microscope (SEM). I want to compare the abundance of a certain type ...
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0answers
16 views

How to fit a distribution to a function of binned values

I am interested in fitting power law or Pareto distributions to a set of values. First, we assume that the abundance $A$ of an organism is related to mass $M$ with a power law with exponent -2: $A \...
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Batch effects in survival data

I have a problem concerning batch effects in survival data of C.elegans. I read through a few forum posts and a paper but I am still not really getting it. In the experiment the effect of different ...
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Predicting the probability of diabetes

I have collected comments of diabetes patients. In these comments they have also mentioned other symptoms. Now patients come to my portal to check diabetes possibilities. User enters x,y,z symptoms. ...