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

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11 views

Programs and procedure for Blackwood test?

I am looking for programs and procedure for the Bradley-Blackwood test, which is normally used to assess test-retest reproducibility.
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11 views

Training models for classification using different negative datasets

I'm working on a massively unbalanced binary classification task - Classification of given protein sequences as belonging to a certain (very small) class, or not. There are about 1,300 positive ...
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1answer
37 views

Any known example of research project being led by statistician in public health

(I am fully aware that my topic may not be relevant here, do let me know if this is true.) I am a research staff with training in epidemiology and biostatistics, working in government organization on ...
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28 views

Good reference book for statistics in medicine

I am looking for a good reference book for applying statistics to medical problems. I am interested in a practical book that describes concepts including statistical power, tests for comparing ...
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1answer
42 views

A Conditional Probability Problem

This is a biological problem, however the problem requires a statistical solution, so therefore I'll keep it as abstract as possible in order for statisticians to be also able to contemplate it - I'm ...
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1answer
28 views

which statistical test to use to compare 3 different types of regions? [duplicate]

I want to compare the percentage of a species in 3 different types of regions. Which statistical test should I use??
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13 views

Testing for significant difference in mortality rate between multiple groups

How do I test for a significant difference between the mortality rate of 4 groups (each group with a different n) group 1: mortality rate = 30.9%, n=55 group 2: mr = 0%, n = 4 group 3: mr = 23.3%, n ...
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1answer
21 views

Creating a translated sample by subtracting mode

Consider a sample $x_1,...,x_n$ which we will call the original sample. To create a translated sample $x_1+c,...,x_n+c$, we add a constant $c$ to each sample point. Let $y_i=x_i+c, ...
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31 views

Project in Bayesian biometrics

I'm working on a project about specific bird species on an island in the Northern Atlantic sea. The data seem reliable and pretty detailed, and range from the 18th century, however their structure and ...
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25 views

what kind of statistic test should I use for my data?

I am working with biological data. The project is about comparing microbiota composition in different samples who have different type of diet. Here is the experimental design of the project: ...
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40 views

What is the null hypothesis in the definition of Sensitivity and Specificity?

I have hard time to understand that what is the null hypothesis in the definition of Sensitivity and Specificity here? I'm student of Statistics and from my little knowledge in this field I can see ...
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21 views

design and analysis of experiments

Kindly recommend some teaching material for "design and analysis of experiments" for the students of biostatistics and epidemiolody. Pls note that the students have only little knowledge on ...
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15 views

How to summarize mean +/- S.D. across disease severity

I am performing a meta-analysis and I have several papers that measure compound X in the blood of patients with a given disease. These papers have classified patients into groups based on disease ...
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12 views

Relation between median follow-up and median survival?

When follow-up is assumed to be constant and variable, is there any relationship between median follow-up and median survival? I.e. should one be less or greater than the other?
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26 views

Cumulative standard deviation calculation

I have a calculated daily survival probability, and associated SE. From this I can obtain the standard deviation. I have to report the cumulative survival over a specific period. So for example, for a ...
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0answers
16 views

Help in interpreting AUC values from ordinal variables

I would appreciate if someone could explain to me the benefit of using area under ROC for evaluating agreements between two raters. Here is an example from two raters on, let's say, clinical time ...
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0answers
24 views

Assumption with alternative hypothesis?

I am testing the reproducibility of two drug concentrations between two sites of the same individual. I am assuming response between sites should be similar. To test the significance I created a ...
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2answers
57 views

Can I use t-test to compare my control and sample mean to confirm significant difference?

My control is a sample without any drug treatment. My samples are treated with drugs. They were both randomly taken from a normal distribution. The hypothesis is $\text{H}_0: \mu = \mu_0$ and ...
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2answers
38 views

Prognostic factor vs. risk factor

As far i understand the difference between Risk factor and Prognostic factor is : Risk factor is the ...
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1answer
55 views

Hypothesis testing with very few data

My biologist friend is having a bad time with her experiment. It's suspected that changing the temperature and organic content in water may affect the growth of crustaceans. In her experiment, two ...
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42 views

Which statistical test to use and why?

My project involves 1) Comparison of new samples against a control and 2) Find any effect on the speed of growth and germination % of seeds by treating them with the new samples My question is, what ...
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1answer
75 views

Problem with identifying outliers

I'm running a biological experiment with rodents, have two groups (each consists of 26 animals), where one is treated with a chemical, and one is control (saline). In one variable, there doesn't seem ...
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40 views

Determining if experiment data can be pooled from multiple experiments

We have a dataset with Time and Treatment as independent variables, and growth volume as a dependent variable. The experiment was repeated on three occasions, with multiple time points and multiple ...
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2answers
176 views

The $z$-test vs the $\chi^2$-test for comparing the odds of catching a cold in 2 groups

I just read in a rather well-respected (popular) science magazine (the German PM, 02/2013, p.36) about an interesting experiment (without a source, unfortunately). It caught my attention because ...
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1answer
147 views

Making a cumulative incidence plot in R

Background I have a survival object in R called km. ...
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1answer
64 views

Defining a threshold for percentage data with high amounts of exact zeros

I am trying to analyse my biological data which is derived from flow cytometry and describes the percentage of cells with a certain property. Data is available for two conditions: once the cells ...
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29 views

Statistical Tests for comparing groups

I am a biologist and I have developed an algorithm that has the ability to identify and quantify fluorescent objects within the nucleus of a cell when imaged in a fixed state under a microscope. The ...
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24 views

Difference between t value and p value [duplicate]

I am not clear about how exactly the p values and t values are used. I know how to calculate them but I am not clear about the basic concept behind them. Any help ?
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42 views

review papers on P-values, adjusted P-values and common statistical tests in bioinformatics

I'm looking for review papers which give comprehensive reviews of P-values, adjusted P-values and common statistical tests in bioinformatics.
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25 views

How to estimate true concentration level of antibodies according to optical density in ELISA?

In ELISA Is it necessary to obtain true concentration level of antibodies for diagnosis? Is there a model allowing us to do so? I know there is a 4-parameters logistic model, but will people ...
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1answer
47 views

Count data with continuous variables

Let's assume one has looked at the occurence of a plant species at different altitude, different temperature and environment. Here are its data: ...
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1answer
75 views

Good introductory biology/genetics readings for statisticians?

I'm looking for books on genetics or biology in general, at an introductory level, ideally where topics are tackled from a statistical point of view. I've been reading "Genes population and languages" ...
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21 views

Diallel Analysis

I apologise for the mix-up. Am trying to do a diallel analysis involving three parents in poultry. I tried using SAS05 program but it didnt work, i guess it was designed for diallel analysis involving ...
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44 views

How to justify using a gamma distribution for biological image analysis

I am trying to characterize objects within the nucleus of a cell. These objects are brighter than the background, and when I remove the background and map the frequency distribution of the objects I ...
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97 views

Understanding formula for the standardized selection ratio (SSR)

Manyl et al defined an index called Standardized Selection Ratio (SSR). Here is the source. I don't quite understand how this index is calculated and how the p.values are calculated. Can you help me. ...
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21 views

Weights for retrospective cohort data

Suppose you randomly identify individuals with a certain disease (cases) at time $T$, then you identify a sample of individuals without disease at time $T$ (but at risk for disease) in a population of ...
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1answer
112 views

Clinical statistic problem

You conduct a case-control study of elevated cholesterol and myocardial infarction (MI). Of 20 MI cases, 10 had elevated cholesterol. Of 30 healthy controls, 10 had elevated cholesterol. These ...
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66 views

Nonparametric test for trend using Python

I am looking to perform a nonparametric test for trend on a continuous outcome across three groups, preferably in Python. For example height (pretend height is not normal) in 4th, 5th and 6th ...
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26 views

One experiment with many (dependent!) hypotheses for motif prediction in dna sequences

I am having the following problem. I have a group of words which are all permutations of each other. On a random dataset of DNA sequences I can calculate the distribution of the number of word ...
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1answer
338 views

Which statistical test should be used to test for enrichment of gene lists?

I have performed an experiment to test the cellular sensitivity to a certain DNA damage agent. We have found 270 genes that were specifically sensitive to the drug and the total number of genes ...
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42 views

Sample size for one sample repeated measures

I am conducting a study in which I want to follow a group of subjects over time. My outcome of interest is continuous and I will measure it at 4 time points. I am trying to calculate the sample size ...
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19 views

Given a matrix, each row with a list of numbers, find the most variable rows with an “interesting” pattern

I have a file that can be considered as a matrix with each row representing a measurement of gene expression of different samples (each column is a sample). I want to find those genes with the most ...
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42 views

Difference between two univariate coverage versus bivariate coverage (ellipse)

I am trying to compare coverages from accounting for two outcomes independently and as a pair. I have 2 sets of p values (p1,p2) from 60 simulations say. I am trying to find out how many times is the ...
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1answer
141 views

Bootstrapping of RNA-Seq data: normal distribution?

I have an RNA_Seq dataset (FPKM values) obtained from the ENCODE Caltech datasets for K562 cells; I also have 6 different lists of genes and I want to show that the expression values of my panel of ...
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1answer
66 views

Pairwise comparisons

I have a situation like this: ...
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1answer
220 views

How to compare two groups when one only has one data point? [duplicate]

I have two groups I want to compare, however, I only have one data point in the first group compared to 450 data points in the second group. Here's the story. I have a patient that has a mutation in ...
4
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3answers
175 views

To what extent can statistics improve patient's treatment?

I was requested by a friend's mother to analyze her data from her past treatment. Since she got leukemia two years ago, she had been instutionlized for various periods and underwent various ...
2
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1answer
66 views

Suitable analysis for my data…?

everyone, I'm new at the statistical analysis so I need some help from more experienced people. I'm working with biological data from gene expression analysis. I have 5 treatments (1 parental toxin; 3 ...
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0answers
49 views

Testing equality of relative frequency ratio in binomial sample

I am sorry if this question is too basic or was somewhere else here on Cr-Validated, but i didn't find anything suitable. I study patients with cancer who were made a byopsy taking to test presence ...
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4answers
247 views

What are the case studies in public health policy research where unreliable/confounded/invalid studies or models were misused?

I am drafting a literature review on a current public health issue where data are confounded: What are common historical case-studies that are used in public health/epidemiology education where ...