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Questions tagged [biostatistics]

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

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Can ANCOVA be used for the following model

Suppose I have 3 treatment groups, and I have pre- and post-treatment test results. There are also 4 covariates which theoreticlaly can influence the post-outcome. So is it possible to find which ...
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6 views

The difference between the cumulative baseline hazard and the cumulative hazard?

I'm not sure what is the difference between the cumulative baseline hazard and the cumulative hazard? Could you please explain it if you are an expert in this field? Thanks
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25 views

Help needed making Random Permutations in R studio [migrated]

I am very new to R and struggling a bit with getting my head around things. I need to make random permutations out of my data set, I have 5 categories (these are age classes) 10, 16, 21, 26, 36. ...
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13 views

Comparison of mutation distribution [closed]

I am wondering about how to compare distribution of point mutation between chromosomes. It is important to take account of length of chromosome. I have 23 chromosomes, and for each chromosome I have ...
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11 views

Sample Calculation of Morisita's Overlap Index

I am actually a biologist who has as question regarding how to apply the Morisita's Overlap Index. I have been told to compare two plant species by using this index and 3 other variables for each ...
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1answer
24 views

Risk prediction equation for disease based on concentrations of circulating proteins

I want to derive a risk prediction equation for disease D based on Pa and Pb, where Pa and Pb are concentrations of circulating proteins in the blood. Disease D has two sub types: Da and Db. In Da, ...
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1answer
22 views

Statistical test for change in prognostic score pre-treatment vs. post-treatment

I am working with medical data and specifically determining whether Treatment_X is safe in certain prognostic groups of patients with chronic liver disease. To summarize: a common prognostic score ...
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13 views

Adjacency matrix of amino-acid residue [closed]

How to get the mathematical representation of the chemical bonds in protein residue or the whole protein? Is it possible to get the connectivity matrix or a pairwise description? The example in the ...
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1answer
30 views

Matching in a case control study

I'm working for a physician who thinks they would like to run a matched case control study, matching on 3 covariates, to assess the effect of exposure to a drug on an outcome. I've never done a case ...
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15 views

Stratify phylogeny based on variables - e.g. which ST are represented by high % males

So I have tree file and metadata. Metadata includes sequence type ST (clusters that correspond in most part to the phylogeny), but also some patient data, age, sex etc. I am trying to identify which ...
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13 views

Can iterative PCA be applied to grouped data?

My data set consist of 156 individuals with fifteen variables. The variables consist of one body mass (dependent) variable and fourteen (independent) variables of different bird bone dimensions (of ...
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1answer
59 views

Controlling for confounding variables in linear mixed effects models (lmer)

I'm using lmer to test how multiple variables (in this case, treatment, species, and sex) influence avian behaviour. ...
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29 views

Confidence interval from sample quantiles

Context I am running some stochastic simulations in R to determine appropriate sample sizes for a biological problem of interest to me. My method iteratively generates "accumulation" curves which ...
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16 views

I squared for measuring homogeneity

I can't seem to find a simple resource that explains what I can use the I2 (derived from Cochrane's Q), often used in meta-analyses for, exactly. Most, if not all resources I find on the subject go on ...
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1answer
26 views

Stuck between ANOVA (with transformation) and multinomial logistic regression

I need help in determining the appropriate stat test to use. I want to know if the 5 treatments (including the control variable) has significant differences based on their Antioxidant Activity as ...
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28 views

What test should one use when dealing with different treatments in plant clones?

In an experiment involving plant clones there are: 20+ treatments, 5 technical replicates for each treatment (plant clones in which the treatments were tested). Variable of interest is Biomass. Due ...
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1answer
19 views

Simple family medical research

The study involved $20$ families, each of $\sim3$ people. For each patient continious parameter $X$ is measured. Each patient has diagnosis $Y=\{\text{ill},\text{healthy}\}=\{1,0\}$. Problem is to ...
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23 views

Different backgrounds, different similarities with ecospat (R language)

I beg all of you your excuses, because the stupid question. I am exploring niche conservatism in five species of Ericaceae. I created two backgrounds sets in order to explore niche similarity (using R ...
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1answer
62 views

Genomics Stats Problem

I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding. I have identified 728 sequences of interest. 597 of these ...
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44 views

biological basis for excluding values outside 3 standard deviations from the mean? [duplicate]

Is there any biological basis for excluding outliers in a dataset of blood cytokine levels (e.g. values outside 3 standard deviations from the mean for each cytokine) as measured by multiplex ...
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8 views

Model for hormone levels over tissue cells

I have a certain type of biological data and I am unsure about how to model it. The data represent the amount of 3 hormones detected along 20 consecutive cells of a certain plant tissue. I think there ...
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1answer
47 views

R code glmer: Different results with same data

I'm trying to run a mixed model analysis and so far I've found two ways to write a negative binomial distribution model for my data: ...
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1answer
64 views

Correcting data using poisson-regression

I'm new to stats and I was wondering if anyone had any good resources that could explain to me: How one can correct their data (false-positives) using Poisson-regression. I've been looking for some ...
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39 views

Warnings using glmer() in R

I'm trying to analyze the differences in the number of plant species found in different types of fields. The number of species per sample is a non-integer because I had to adjust the number to account ...
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23 views

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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12 views

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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2answers
26 views

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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20 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
82 views

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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14 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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36 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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0answers
18 views

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
28 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
42 views

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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12 views

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
35 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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50 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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0answers
17 views

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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36 views

Linear model from iterative process in R

I would like to test a relationship between to factors such as birds occurrence and temperature for instance, to test if temperature affects birds occurrence from a country (e.g. Germany). I have a ...
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24 views

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
37 views

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
121 views

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
34 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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31 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
12 views

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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21 views

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
41 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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0answers
13 views

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 ...