Questions tagged [genetics]

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

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Is there a test or function to perform multiple comparisons for a big dataset?

I have a big dataset of 2304 values : 384 different genes expression values in triplicates and for 2 different groups (ie, different treatments). I only want to compare the same genes between the 2 ...
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Comparing two groups by the counts of their features

Imagine there are two different groups of individual samples. I know they are different but I don't know why. For example in biology a group of sick individuals and a group of healthy ones. Now for ...
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Understaning Fisher’s combined probability test in my analysis

I'm trying to understand Fisher's combined probability test, especially how I used it in my analysis. I have 25 datasets, each one containing genomic data from cancer patients. I conducted a ...
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Statistical Genetics - How to interpret data & analysis

My question is how to interpret $G_{ij}$ in the following statistical genetic model $$h(\mu_i) = \alpha_0 + \alpha'X_i + \beta'G_i,$$ where $G_i = (G_{i1},\dots ,G_{im})$ are allele counts (zero, one, ...
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Multiple comparisions between sexes within years ANOVA or t-tests? Tukey posthoc? Bonferroni?

I am conducting a genetic analysis comparing Fst and relatedness coefficient values between male and female animals across years from 2013-2019. Each year is divided into quarters, so I have a total ...
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Having trouble with my analysis. I have no one to ask. I thought I would post here

I performed an experiment where I shocked fish eggs at different times prior to first cellular cleavage, this was to create tetraploid fish larvae. I have a control group and then 9 treatments (60, 65,...
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Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change calculated

I have a microarray dataset that has already been normalized, and the fold change values for each gene in the mutant versus the wild type have been calculated. I'm interested in determining the ...
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Question about variance explained and group differences

A heritability statistic, as I understand it, describes the percent of variation in a trait that is attributable to genetic variation, with the rest attributable to environmental variation. I've heard ...
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Effect attenuation with adjustment

Typically in genetic studies, sensitivity analyses are used to quantify how estimates of genetic effects are affected by adjusting for additional covariates $Z$. So we have separate regressions for a ...
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Calculate the influence of multiple mutation in the quantitative levels of a protein

My experiment is based on quantifying levels of B12 vitamin in a sample of patients retrospectively selected based on values that can take (under our criteria): normal low levels: under the ...
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Statistical significance in known population

I am working with a data set with the sequence identity (a value in [0,1] representing the conservation between sequences) of many genes for many bacterial strains. I would like to be able to draw ...
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Chi-square in genetics with fruit flies. Getting 0 observed when the expected was more than 0, and got an unexpected phenotype. How to handle?

We crossed fruit flies in genetics class and I ended up with very different results than the expected values. For some values, I had 0 observed when the expected was more than 0. Would I go through ...
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Power calculation: What does it mean if the observed effect size is lesser than the expected effect size in power calculation?

I am conducting a regression analysis on TNF-a in relation to a genetic marker. I performed a post-hoc power calculation using a software called Quanto. The mean(SD) of my outcome variable is 34(14). ...
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Estimated standard deviation of a phenotype prevalence that is derived from several studies

I have allele frequencies from two independent studies Study Number Sample Allele 1 Freq Allele 2 Freq Allele 3 Freq A 20 .45 .475 .075 B 34 .72 .28 NA The weighted average of each allele ...
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Should I include a constant term when testing the significance of variables against a null model?

I have a one-hot vector $y \in \{0,1\}^{n}$ giving the case/control status of a group of genetic samples. I also have a genetic vector $G \in \{0,1,2\}^{n}$ and a vector of covariates $K \in \mathbb{R}...
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How to compare two ranked lists of genes with ranking values?

I have 80 independent sets of genes with 6000 genes in each. Gene expression values are ranked and scaled from 0 to 1. So, a set looks like this: Gene1 1 Gene2 0.98 Gene3 0.85 ... Gene5998 0.002 ...
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Apparent artifact in R volcano plot of hazard ratio vs. p-value

I've used R and the survival package's coxph() function to calculate hazard ratios and p-values for around 20,000 genes using data from The Cancer Genome Atlas. When I plot the hazard ratios and -...
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Calculate significant genes from significant level

If I know that in a study a total of 2936 associations reached a given statistical significance level (P < $6\times 10^{-11}$) and that the total number of SNPs analyzed that belonged to a specific ...
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Estimating heritability from twin studies--How to get it?

I was learning the concept of heritability, and come to the Falconer's formula: $h^2=2(r_{MZ}-r_{DZ})$                               (1) Where $r_{MZ}$ and $r_{DZ}$ are correlation coefficients of ...
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Asserting parentage likelihood based on SNP data

Let's say I have a population of N specimen that I've succesfully genotyped by M SNPs. If I know allele frequencies for every SNP, how do I compute likelihood of parental link (e.g. mother-daughter) ...
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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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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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Can I use a binomial test in this situation?

A bit of context: Basically, I'm working with a list of genetic positions of interest (n = 358) which have, among them, a number of specific positions (n = 63) that are related to some genes (let's ...
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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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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 ...
Joey Portier's user avatar
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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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What does it mean if a simple linear neural network performs better than an LSTM on sequential data?

I'm working on a genetic data project, where one data sample is represented as sequences of integers (of length 2000) and it needs to be classified into one of 4 classes, so I guess it is similar to ...
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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 ...
Pros's user avatar
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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 ...
Jónás Balázs's user avatar
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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 ...
Idiotsum's user avatar
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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 ...
mintypasta's user avatar
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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 ...
curious_dan's user avatar
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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 ...
statssyboy's user avatar
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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 ...
Brent Brookes's user avatar
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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 ...
German Demidov's user avatar
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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 ...
user3687798's user avatar
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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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