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Questions tagged [biostatistics]

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

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14 views

Which statistical studies should be carried out for expression analysis of genes when I have fold change data of genes

I am new to R and data analysis. I am working on gene expression. My data frame contains Gene_ID and quantification_value which is the fold change of the gene. ( the value represents the amount by ...
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20 views

Differences between cumulative link models (ordinal) and multinom (nnet) for fitting multinomial data

I'm trying to understand cumulative link models and how they differ from multinom models in R. Here's a simple example of a multinom model and plot output using the nnet package: ...
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34 views

Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers? [closed]

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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21 views

How to determine degrees of freedom for regression when not all observations are independent?

I'm trying to determine the degrees of freedom for my dataset. (Purpose: to determine the confidence interval for the slope of the regression line.) The problem is, the explanations of degrees of ...
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1answer
46 views

Splitting of bimodal distribution, use in regression models

I have a bimodal length-frequency distribution for the females of a species with a one-year life span. This pattern is not observed in the males. I suspect that the bimodality is due to different ...
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8 views

What is the probability of regex pattern occurrence in a string of length n?

I have a string of length n, composed of 20 characters of equal probability. What is chance of occurrence of a regular expression pattern, like 'WP[^WFHY]{5}W' by chance? In case you are not familiar ...
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1answer
42 views

Response is count and the first explanatory is binary second is continuous. Which GLM should I use?

So I've got a response variable with count data e.g. number of species found and two explanatory. The first is a treatment I did or did not applied -> Yes or No, so binary. My second explanatory would ...
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9 views

log values in coxph model?

I have a data frame of gene expression values (sequencing). When I do CPM-normalization without doing log2, I get much "better" (lower) p-values compared to when I do log2-CPM. What is the ...
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1answer
25 views

Attirbutable risk from competing risks

There are a number of ways to estimate attributable risk fractions from Cox regression and logistic regression. Does anyone know how to estimate attributable risk from a competing risks regression ...
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10 views

How to properly perform “change from baseline” (pre-post) analysis adjusting for pre using lme4 in R?

Let's assume I have the following data set, consisting of pre (t1) and post (t2) measurements. I want to check, if there is a significant effect over time (t1, t2). ...
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1answer
17 views

Test that at least one hazard is greater than hazard in control

I have an experiment with one control and three experimental arms, A, B and C. My experiment generates survival data. I have survival times for each group, $T_{tj}$, where $t = \{ control, A, B, C\}$ ...
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1answer
72 views

Probability of multiple parasites given the presence of one parasite

I am trying to simulate parasitic plants that infect trees. I would like to test wether the presence of one parasite makes it more likely that the tree has more than one parasite. The number of trees ...
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1answer
21 views

How to cut features with large amount of 0 values from high dimensional data?

I have genomic data (miRNA) that is high dimensional: $198$ samples and $1584$ features. ...
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1answer
78 views

Student t-tests — please verify if I'm using it correctly for feature selection

I have a $198$-sample dataset containing miRNA types (numerical features) and one categorical feature "Type" with values "Tumor" or "Healthy". ...
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85 views

Interpreting snake-like structures in the UMAP visualization of a FASTA data set

I'm looking for some guidance to interpret a UMAP plot. I started with two FASTA files for two different genes. I concatenated everything into a single string of only ACGT. Then I split that ...
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16 views

Time-to-event statistical test for toxicity within a 12-month time frame?

I am performing a retrospective study and this is my hypothesis: among patients with metastatic melanoma, antibiotic exposure within the 3 months prior to immunotherapy increases the risk of therapy-...
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2answers
47 views

Creation of contigency table and calculation of effect size (Chi2, Cramer's V)

I am a bit unsure in my approach of applying the Chi2 GOF test to my data and calculating the correct effect size. The situation: I am studying the occurrence of specific biological phenomena in ...
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15 views

Bias of Pearson correlation estimator of two Bernoulli variables

Crossposting link: https://math.stackexchange.com/questions/3312349/bias-of-pearson-correlation-estimator-of-two-bernoulli-variables Suppose we have two correlated Bernoulli random variables, $X_j$ ...
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1answer
27 views

Analysis of multiple response/check all that apply survey data

I am helping to review a manuscript and suffering from mental block on some data analysis. The data in question is from a cross-sectional survey, a health care provider KAP (knowledge, attitudes, and ...
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10 views

How can I get the sequence logo = C in the first column of the DNA analogy of the book “Machine Learning - A Probabilistic Perspective”

section 2.3.2.1 of book "Machine Learning - A Probabilistic Perspective" uses this Figure to illustrate the application of multinomial models Figure 2.5 (a) Some aligned DNA sequences. (b) The ...
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1answer
42 views

How to measure interaction between variables (mutations)?

I have a large dataset of germline genetic mutations from a population of 1,000 individuals both affected and non-affected. I've already looked into individual mutations that are enriched in the ...
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13 views

Comparing means between 3 different groups across time (given that the 3 groups are defined by 2 factors)

I have 3 different experimental groups: 1) Wild-type, control 2) Transgenic, control 3) Transgenic, Drug-treated Therefore, my groups are defined based on two factors: genotype and drug treatment ...
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1answer
56 views

What do ellipses of PCA analysis (factoextra) mean?

Biological question: do plants that have been attacked by insects differ in their characteristics from plants that have not been attacked by insects? Data frame includes six numerical variables ...
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8 views

RNA-seq: probabiliy of at least one type I error

I need to find a mathematical expression for the probability of finding at leat one type I error. I know that in general that probabilty is: P=1-(1-a)^m. With a being the probabily of making a type I ...
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4 views

Stratified Log Rank Test with Unequally Sized Strata

If I perform a stratified log rank test in a situation with many strata (currently I have 8), in 6 of the 8 there are very small numbers (i.e., 1 or 2%), but the other strata are fairly balanced, how ...
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2answers
92 views

How to get confidence intervals for Patient-Years?

In medicine patient-years is a popular concept. Example: $100$ patients are followed for $2$ years. In this case, there are $200$ patient-years in total. If there were $8$ myocardial infarctions in ...
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2answers
51 views

Cox regression different results with different combinations of variables

I need help understanding how to use cox hazzard model to calculate risk of death in data from a cohort study. I have a set of data on physical activity and I want to do a cox regression on ...
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1answer
53 views

What is the equation to calculate the sample size for A/B testing? [closed]

I have been searching for information on how to calculate sample size for A/B testing. My research was fruitless. I found many online calculators, but not any blog/paper that explains how the ...
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1answer
19 views

How to find difference between data recorded for 1431 variables for X subjects, across 3 time points?

I am doing research using magnetoencephalography (MEG). I'm performing coherence analysis which, briefly, is a measure of neuronal synchronicity and functional connectivity. For each subject scanned ...
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44 views

Converting annual survival rate to daily mortality probability

In a peer-reviewed paper, I came across the following conversion: Yearly survival rate -> 0.70 The authors have calculated the daily probability of death using (1 - 0.70^(1/365.25)) = 0.000976 ...
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1answer
48 views

How to test whether individual fits to regression line or not

I have a defined regression model for the healthy control (HC) group, with corresponding CIs of coefficients and of E(Y). I would like to test whether individuals belonging to another population (...
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1answer
42 views

Is this an example of where I shouldn't scale before doing PCA / PLS?

I'm working with NMR spectra (it's a common chemical test). There are various peaks of the signal across a range of ppm values. I'm trying to relate the NMR spectra of various samples to a ...
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10 views

Chargaff's rule and degrees of freedom of the chisquare

I have a question regarding if and how one should take into account for the extra knowledge that he/she has of a model when determining the degrees of freedom of a distribution, in my case the chi-...
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1answer
50 views

When knowledge of one event tells us nothing about another

I have an example; Say I have two genes on two different locations on two different chromosomes. P(A) = gene is from location 1 P(B) = gene is from location 2 Geneticists believe that knowledge of ...
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1answer
30 views

What type of a test will I perform in R?

I have a dataset which contains data observed for patients who were hospitalized for moderate or severe infection and given one of two antibiotics. The number of days each patient was hospitalized ...
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2answers
166 views

Cox proportional hazard analysis with non-uniform samples; power analysis

We have a study involving 10,000 patients, 5,000 of them treated with drug A and 5,000 with drug B. We want to know if drug A is more effective than B. The median time to event (death) after treatment ...
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1answer
60 views

sample size calculation in 3-arm survival analysis

In a 3-arms clinical trial, with time to event data, either A is superior to C or B is superior to C it will be considered significant. No need to compare A and B. I know how to calculate the sample ...
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42 views

Choosing appropriate statistical tests

I am trying to run stats on medical treatment data and would like your guys and girls help Goal: Comparing two trends of annual percentages for statistical significance. Is one decreasing due to the ...
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1answer
19 views

Batch differences in biochemical measurements - statistical solutions?

I'm working with inflammatory markers from human participants in a current study and have been stumped by between-batch differences. One third of the participants had their inflammatory markers ...
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17 views

How to identify the difference in significance of two different z test for two proportion test?

I have two cell types (A and B) in a tissue. I have 5 replicates of RNA sequencing data in control and treatment condition for cell type and B separately. We are interested in identifying genes which ...
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1answer
90 views

Given two related ratios within a population, derive a third ratio (eg. redheads, non-redheads, and skin cancer)

If People X are N times more likely to have attribute A than non-X People X are P percent of the population then What percentage of A's are X? Example (the numbers are just for illustration). If ...
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1answer
57 views

What test do I use for this? (NOOB biostatistics question)

Suppose I have some subjects and I give each of them a test. I would end up with a dataset like: ...
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0answers
29 views

Rank non-normally distributed sets of integers: long read sequencing and phase blocks

I have about 20 arrays of empirical integer values, which are each not normally distributed, with long tails. I am looking for a 'sane and sound' metric on how to sort these distributions, "with ...
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1answer
26 views

Log transformed data

When you log transform data what is being tested on the original scale of the data? And why can we use our log transformed data to answer our scientific question? We are looking at data comparing ...
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0answers
34 views

How can I isolate objects from a 3D image volume using normally distributed geometric features

I have '.tif' image stacks that I am analyzing as volumes. For every object, I can get the Volume, surface area:volume, 'sphericity' and Euler number. For every one of those features, the objects I am ...
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20 views

Emergence of Lognormal distribution for the concentration of chemical compounds

I'm currently reviewing the literature about lognormal distributions describing/approximating the variability of a given chemical compound across different cells/ samples etc etc. The main argument ...
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21 views

Statistical testing in clinical research

I just did a univariate binary logistic regression to classify a disease based on some medical parameters. Now only one variable showed significant result (p-value < 0.05). Assuming sufficient ...
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1answer
214 views

How to use Cullen and Frey graphs for downstream statistical analysis? [closed]

How to use Cullen and Frey graphs for downstream statistical analysis? I do not see any difference in normalized and raw data Cullen and Frey plots! Raw data ...
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6 views
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20 views

Model for missing data at baseline?

I am interested in looking at the effects duration of a certain medicine has on an outcome over time assuming the effects to be nonlinear. Some people would have baseline data of before starting ...