Questions tagged [genetics]

The scientific study of the principles of heredity and the variation of inherited traits among related organisms.

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Regressing on nuisance features as pre-processing

A friend recently told me about a technique to remove the effects of an unwanted feature $x$ in a response variable $y$. He mentioned an example from genetics. By regressing $y$ on $x$ (or a ...
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Monty Hall and a Mendelian F1 monohybrid cross

I'm reading a biology textbook and I also happen to have read the Monty Hall Problem article on Wikipedia recently. I'm a middle aged layperson. (Been a long time since anyone's taught me anything so ...
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Multiple mice (subjects) grouped by genotype (condition) with multiple measurements per mouse

I am trying to analyze fertility data for a cohort of mice with several different genotypes and I am stumped. 3 mice have genotype A, 3 have genotype B, and so on. Each mouse has several litters over ...
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Standardisation with respect to controls

When performing analyses using polygenic risk scores (PRS), Why is it important to standardise/normalise PRSes using mean and sd derived from control samples, before performing analyses, such as ...
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I have to adjust p-value in One way ANOVA with 3 groups and 600 metabolites?

I have three groups: CC, CT and TT and 600 metabolites. When I do a lot of t-tests, I have to adjust the p-value, for example with fdr, but when I do a ANOVA with 3 groups, have I to adjust the ANOVA ...
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How to interpret results from cov2cor() function in R/sommer package_genetic correlation estimation?

I'd like to calculate the genetic correlation of plant height from same individuals between two different ages using linear mixed model. In the model, the fixed effect was experimental design and the ...
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What are the different ESS (Effective Sample Size) methods in arviz?

I am running a Markov Chain Monte Carlo sampler for phylogenetic inference. I used to track the progress of convergence by checking the Effective Sample Size in Tracer. Because the results started to ...
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Optimum number of PCs to retain when finding BIC

I am using the Bayesian Information Criterion (BIC) to find my optimal value of clusters (k) in a dataset of 1774 individuals with each 5903 SNPs. I used the following R code from the adegenet package:...
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Randomization-based test for comparisons of an observed proportion against an expected distribution

I generated a dataset of organisms and their gene organization, divided into groups of severely unequal sizes. My goal is to statistically compare each group's proportion of unique gene organizations ...
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Unsure how to analyze count data. Plot the logarithm?

My experiment consisted in turning off multiple genes separately from each other and counting a certain type of cells (say cells A). For each gene I had around 20 organs for which I counted cells A. ...
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Computing BIC and other methods to find most likely K cluster

I have recently been diving into the world of population genetics and still remain with some questions when trying to conclude what the most likely value of K for my dataset would be. To give you some ...
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Adding covariates to a regression analysis of genetic data

I have 2 covariates in my data which are SEX and RACE. My data is genetic data and SNPs. Is adding Principle Component Analysis(PCA) as a covariate in the regression model is better than adding the ...
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voom mean-variance plot has set of genes where variance increases with expression level

I'm using limma + voom to model an expression dataset, but I'm observing a weird subset of genes where the standard deviation increases with the expression level rather than decreasing as is the case ...
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Repeated Measures Mixed model Design

I am trying to model gene count data from an RNA seq experiment. In the experiment subjects were selected from 2 predefined groups. 5 Subjects from group A and 10 subjects were selected from B. For ...
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Compare gene coverage across group o samples

Hello, I have a matrix data where rows are samples(40 in one group and 40 in the other), columns genes(20k) and the value is the coverage. Like this Sample Group Gene1 Gene2 Gene20000 S1 A 100 200 .....
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Fisher's Exact Test for 2x2 Table with Random Zero

I'm trying to determine if the rate of mutation for a particular gene is significantly different between two groups (primary tumor and metastases) with Fisher's exact test and so my contingency table ...
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Justification of the Bonferroni correction

I've come across the Bonferroni correction in a genetics course. I understand the idea that we need to account for type I errors, but I can't fully get my head around it. In the genetics scenario, it ...
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simple simulation of recurrent gene mutations

Sorry if this question is too basic for the forum. I am trying to determine the number of recurrently mutated genes expected by chance given an equal likelihood of mutation for all genes. There are ...
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Better to use wald test or likelihood ratio test to make pairwise comparisons after omnibus test in this scenario

I am testing the association between a gene and a binary disease. The gene has many different "versions". These versions are called alleles.I am also including covariates for sex, age, etc. ...
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Is it possible to go back and do pairwise comparisons following an LR test, if so what is the correct way

snp1, snp2, and snp3 are "versions" of geneA. I want to determine if geneA significantly effects disease. I have sex as a potentially confounding factor. If geneA affects disease I want to ...
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Cox analysis and data interpretation

I am doing some statistical analysis using Kaplan curve and cox analysis on a list of genes combining them with a single marker. At KM curve these genes behave in different ways in terms of whatever ...
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Type of ANOVA test?

I am trying to generate an ANOVA to test if a particular genotype (A=mutant, B= Wild-Type; control) is salt sensitive by measuring primary root length in four different medias (1=mock, 2=salt, 3=salt ...
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Frequency of mutants in a very large number of observations

During cellular division (generation of two cells from one) bacteria experience mutations, where a newly produced cell harbors altered genetic code. To measure the rate of this happening Max Delbrück ...
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What is the distribution of genotypes of AB0 blood types given the phenotype

Let's assume we only have the distribution of the phenotypes for a given population. Let's take Hungary as an example. According to Wikipedia $P(0) = 36\%$ $P(A)=43\%$ $P(B)=16\%$ $P(AB)=5\%$ Let's ...
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How to do ANOVA analysis for therapeutic biomarker screening for drug sensitivity

I am new to Bioinformatics. The graph below (from GDSC database) is to find therapeutic biomarker for drug sensitivity. I wonder how to do this kind of ANOVA analysis on my own so as to make this kind ...
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ACE model in R's `lmekin` package

I am trying to run an ACE twin genetics model in R using the package lmekin. I am trying to run the ACE model as described in ...
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What are the consequences of using year of birth, rather than age, as a covariate in logistic regression?

Would this affect the estimates of other effects in the model? Would it affect the estimated impact of age/YOB? I have a cohort but since they are all recruited at different times, I don't know which ...
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Calculation of degrees of freedom for chi-square test

I am not sure how to calculate the df for the following data: The data is for a cross between flies to see if the observed phenotypic ratios are following the predictions of Mendel's laws. The total ...
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How do I calculate the expected value of a binomial distribution for a genetics example?

I have model with 20 genes which can take on a value of 1 or 0 (the alleles). What is their expected value and variance assuming the alleles are selected with equal probability? Is this just a ...
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Can I choose a subset of ordered effects when doing multiple hypothesis testing?

I have a question about multiple hypothesis testing. Suppose I calculate an effect for 2000 gene on some outcome. I order those effects, and only take the top 10 genes according to effect. I only ...
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PCA clustering and creating a new covariate for RNAseq

I am currently doing an RNAseq experiment and some quality control on data. I noticed that there seems to be some kind of batch effect that I cannot explain from the variables I already have. I've ...
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Is there a way calculate a gradient of dissimilarity across multiple sites using presence/absence data?

I’ve been trying to come up with a metric for species (dis)similarity for fish in a series based on presence or absence data that gives a value of 1 or 0 for each lake. From my research, it seems like ...
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Statistical method for estimation of Penetrance

I was thinking on a problem: there is a rare disease, associated with some ultra-rare genomic variant (which means ~ 1 out of millions), and there are estimations of penetrance (how many individuals ...
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Categorization of continuous predictor in logistic regression

I have one continuous variable GENETIC SCORE and one binary variable HEALTH (case vs control i.e. 0/1). I want to fit a log regression model to this data to get the odds ratio for different percentile ...
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2 answers
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Binomial proportion confidence interval when rigid bounds on population proportion (0.5 < p < 1)

A standard problem is estimation of confidence intervals for a population proportion given that one has observed f successes out of n independent trials. There is a reasonable discussion of this ...
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What is penetrance and why is a family study needed to estimate it?

In this statistical genetics article, the authors discuss the issue of not knowing the cancer penetrance of a certain gene variant. They say this is because families with disease history are more ...
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Statistical significance in mutations in two groups

I'm doing an analysis examining the mutations of a set of ~3 genes in 4 different populations. For Gene 1: In Group A 33/540 have that mutation, Group B 66/100, Group C 15/213, and Group D 20/32. And ...
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ATGC sequence of gene expression data [closed]

I am not a pro in genetics so please excuse my non-technical language. I need dataset which contains the gene expression as well as the associated ATGC sequence with each gene expression value. For ...
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Poisson and Gamma distribution for testing randomness

In genetics I want to test whether InDel (insertion and deletion in DNA) sizes occurs with the same probability. I heard that I should gamma distribution to model it. I found ...
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Calculating heritability: pedigree information with family variation

currently I am aiming to calculate heritability, for which I would have to estimate additive genetic variance (the inverse of the relatedness matrix) for a first step. This is done with the following ...
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How should I interpret a weighted genetic risk score?

I created a weighted Genetic Risk Score (GRS) by summing the product of the SNP-dosages times their regression coefficients from the GWAS in which I found them. So: ...
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1 vote
1 answer
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Linear Regression Approach For Trends

I'm working on a project with genetics but I think my problem is applicable to general statistics. I want to test frequency (Minor Allele Frequency) of a SNP/variant across 5 age categories to see ...
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1 vote
1 answer
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A question about pca and gene function analysis

I'm new to bioinformatics, and I have a pretty basic question. Let's say I have a bunch of genes {Xi} and I want to know which one has the most significant on some measurable phenotypic trait Y. Now I ...
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1 answer
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How do children manage to pull their parents together in a PCA projection of a GWAS data set?

Take 20 random points in a 10,000-dimensional space with each coordinate iid from $\mathcal N(0,1)$. Split them into 10 pairs ("couples") and add the average of each pair ("a child") to the dataset. ...
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2 votes
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SKAT test statistic differences

I am trying to implement the SKAT test statistic(from the paper Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test). According to the paper the test ...
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1 vote
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Interpreting PCA, comparing genetic structure within mice population from two continents

I'm interested in comparing the intra-regional genetic relatedness between two populations of mice. One population is native to Europe, while the other is native to North America. I ran PCA to find ...
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2 votes
1 answer
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To find p-value of compounds

I have next SNPs data.frame structure ...
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3 votes
0 answers
132 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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Is it wrong to standardise a variable and then centre it for use in multiple regression? [duplicate]

Is it wrong to standardise a variable (e.g. polygenic risk score) and then centre it for use in multiple regression?
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Avoiding pairwise analysis in count data?

I'm having some trouble choosing an appropriate analysis method for some count data that I have. I'm looking at mutation counts in 50 genes across 6 related disease states. Counts range from 0 to ~400 ...
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