Skip to main content

Questions tagged [genetics]

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

Filter by
Sorted by
Tagged with
2 votes
0 answers
31 views

Problem regarding False discovery rate correction for multiple comparison

I am conducting research to find association of a gene with a disease. It's a case-control study. I have divided the cases into groups A and B based on genotype and controls into groups C and D. I ...
Confused_biologist's user avatar
0 votes
0 answers
56 views

gene total volume test

1, I want to compare the FGF gene total expression level (sum level from all the cells) in two groups of cells. Suppose group A has 500 cells and group B has 100 cells. 2, gene FGF level in the two ...
coding_something's user avatar
1 vote
0 answers
27 views

Bayesian multivariate regression with repeated measures

I am trying to estimate variance components (specifically, genetic correlations) using mixed-effects models. My random effect is subject id and my dependent variables y1 and y2 are categorical scores ...
Nicole's user avatar
  • 11
0 votes
0 answers
17 views

Negative bete value for Polygenic Risk Score (PRS) caiculation

I am learning to calculate the Polygenic Risk Score (PRS) for a disease. However, I am confused about the $\beta$ used in the formula: $$ \text{PRS} = \sum_{i=1}^N \beta_i\times G_i $$ $\beta_i$ is ...
Lyn's user avatar
  • 35
0 votes
0 answers
11 views

Why or When is between-group variance equal to the covariance among members of a group?

In Introduction to Quantitative Genetics (Falconer) , one of the ways of estimating heritability of a trait is by using a full-sib/half-sib model. In a full-sib/half-sib model, a number of males are ...
S. Sasindran's user avatar
0 votes
1 answer
25 views

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 ...
user avatar
0 votes
1 answer
55 views

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 ...
lesolorzanov's user avatar
2 votes
0 answers
41 views

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 ...
Programming Noob's user avatar
0 votes
1 answer
59 views

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, ...
Kevin's user avatar
  • 3
0 votes
1 answer
42 views

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 ...
Kyle Finn's user avatar
1 vote
0 answers
52 views

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,...
LUUPE's user avatar
  • 11
1 vote
0 answers
39 views

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 ...
ucb's user avatar
  • 11
1 vote
0 answers
22 views

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 ...
nuwio4's user avatar
  • 11
0 votes
0 answers
13 views

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 ...
user36302's user avatar
  • 143
0 votes
0 answers
26 views

How to generate significant level for the following data (Fisher exact)

I have a categorical data that I don't know how to generate the significant level. Row = Group A and Group B; Column = Unchanged, upgrade, downgrade (From left to right) 7 6 4 4 0 6 I tried to run ...
Ivan Leung's user avatar
1 vote
1 answer
43 views

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 ...
Rachel's user avatar
  • 13
0 votes
0 answers
92 views

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). ...
arshad's user avatar
  • 863
0 votes
1 answer
44 views

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 ...
curious's user avatar
  • 115
1 vote
0 answers
71 views

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}...
Jeff's user avatar
  • 11
0 votes
1 answer
179 views

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 ...
Yulia Kentieva's user avatar
2 votes
1 answer
272 views

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 -...
oncologystats's user avatar
0 votes
0 answers
25 views

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 ...
katara 's user avatar
  • 111
0 votes
1 answer
125 views

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 ...
Raymond's user avatar
  • 11
1 vote
0 answers
34 views

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) ...
Daniil Khlebnikov's user avatar
2 votes
1 answer
222 views

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 ...
Mete Yuksel's user avatar
0 votes
0 answers
30 views

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 ...
user avatar
2 votes
1 answer
316 views

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 ...
Alex's user avatar
  • 185
0 votes
1 answer
315 views

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 ...
Annamaria Porreca's user avatar
1 vote
0 answers
60 views

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 ...
elielink's user avatar
  • 111
3 votes
1 answer
856 views

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 ...
Anaphory's user avatar
  • 191
0 votes
0 answers
152 views

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
1 vote
0 answers
295 views

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 ...
Jautis's user avatar
  • 21
0 votes
0 answers
46 views

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 ...
Elouise_K's user avatar
0 votes
0 answers
728 views

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 ...
Ronny's user avatar
  • 1
0 votes
1 answer
203 views

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 ...
Tee's user avatar
  • 1
1 vote
1 answer
29 views

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 ...
stchlk's user avatar
  • 11
1 vote
1 answer
581 views

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. ...
curious's user avatar
  • 115
0 votes
0 answers
17 views

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 ...
curious's user avatar
  • 115
0 votes
1 answer
56 views

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
  • 1
1 vote
0 answers
44 views

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 ...
user301034's user avatar
2 votes
1 answer
94 views

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 ...
Treex's user avatar
  • 144
2 votes
0 answers
37 views

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
0 votes
1 answer
283 views

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
1 vote
0 answers
125 views

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 ...
JDoe2's user avatar
  • 680
1 vote
0 answers
165 views

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
0 votes
1 answer
734 views

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 ...
degmez's user avatar
  • 21
1 vote
1 answer
212 views

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 ...
adkane's user avatar
  • 1,021
0 votes
1 answer
23 views

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
0 votes
1 answer
140 views

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
0 votes
0 answers
213 views

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

1
2 3 4 5