Statistical Analysis Stack Exchange
Statistical Analysis Stack Exchange

Questions tagged [genetics]

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

Reference for tag wiki excerpt.

What is Genetics?

by By Dr. Ananya Mandal, MD (published originally in news-medical.net)

"Genetics is the study of heredity. Heredity is a biological process where a parent passes certain genes onto their children or offspring. Every child inherits genes from both of their biological parents and these genes in turn express specific traits. Some of these traits may be physical for example hair and eye color and skin color etc. On the other hand some genes may also carry the risk of certain diseases and disorders that may pass on from parents to their offspring."

A Brief History of Genetic Science and Regulation by gmeducation.org

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Feature selection for "final" model when performing cross-validation in machine learning

I am getting a bit confused about feature selection and machine learning and I was wondering if you could help me out. I have a microarray dataset that is classified into two groups and has 1000s of features. My aim is to get a small number of…
danielsbrewer
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Correcting p values for multiple tests where tests are correlated (genetics)

I have p values from a lot of tests and would like to know whether there is actually something significant after correcting for multiple testing. The complication: my tests are not independent. The method I am thinking about (a variant of Fisher's…
Stephan Kolassa
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How likely am I to be descended from a particular person born in the year 1300?

In other words, based on the following, what is p? In order to make this a math problem rather than anthropology or social science, and to simplify the problem, assume that mates are selected with equal probability across the population, except that…
xpda
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In genome-wide association studies, what are principal components?

In genome-wide association studies (GWAS): What are the principal components? Why are they used? How are they calculated? Can a genome-wide association study be done without using PCA?
suprvisr
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Calculating the probability of gene list overlap between an RNA seq and a ChIP-chip data set

Hopefully someone on these forums can help me out with this basic problem in gene expression studies. I did deep sequencing of an experimental and a control tissue. I then obtained fold enrichment values of genes in the experimental sample over…
stlandroidfan
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How does quantile normalization work?

In gene expression studies using microarrays, intensity data has to be normalized so that intensities can be compared between individuals, between genes. Conceptually, and algorithmically, how does "quantile normalization" work, and how would you…
Stephen Turner
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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. Then do PCA on the resulting 30 points and plot…
amoeba
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Soft-thresholding vs. Lasso penalization

I am trying to summarize what I understood so far in penalized multivariate analysis with high-dimensional data sets, and I still struggle through getting a proper definition of soft-thresholding vs. Lasso (or $L_1$) penalization. More precisely, I…
chl
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The use of median polish for feature selection

In a paper I was reading recently I came across the following bit in their data analysis section: The data table was then split into tissues and cell lines, and the two subtables were separately median polished (the rows and columns were…
posdef
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Power analysis for survival analysis

If I hypothesize that a gene signature will identify subjects at a lower risk of recurrence, that is decrease by 0.5 (hazard ratio of 0.5) the event rate in 20% of the population and I intend to use samples from a retrospective cohort study does the…
user712
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Enrichment analysis by gene duplication level

Biological Background Over time, some plant species tend to duplicate their entire genomes, gaining an additional copy of each gene. Due to the instability of this setup, many of these genes are then deleted, and the genome rearranges itself and…
TDN169
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Why would one use age-squared as a covariate in a genetic association study?

Why would one use age and age-squared as covariates in a genetic association study? I can understand the use of age if it has been identified as a significant covariate, but I am at a loss as to the use of age-squared.
Kevin
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How to calculate Standard Error of Odds Ratios?

I have two datasets from genome-wide association studies. The only information available is the odds ratio and the p-value for the first data set. For the second data set I have the Odds Ratio, p-value and allele frequencies (AFD= disease, AFC=…
Bernabé Bustos Becerra
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How to calculate confidence intervals for pooled odd ratios in meta-analysis?

I have two datasets from genome-wide association studies. The only information available are the odd ratios and their confidence intervals (95%) for each genotyped SNP. My want to generate a forest plot comparing these two odds ratios, but I can't…
BIBB
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