The genetics tag has no wiki summary.
23
votes
6answers
2k views
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 ...
4
votes
2answers
525 views
How to visualize/summarize a matrix with number of rows $\gg$ number of columns?
I have a matrix of positive real numbers between 0 and 1; the rows represent genes and columns represent samples. Number of rows is greater than the number of columns by a magnitude of $10^4$. I am ...
4
votes
1answer
2k views
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 ...
1
vote
1answer
316 views
What is the difference between independence.test in R and Cochrane and Armitage trend test?
What is the difference between independence.test in R and CATT (Cochrane and Armitage) tests?
How these tests are calculated?
Where do we and how do we define ...
14
votes
4answers
3k views
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 ...
4
votes
3answers
2k views
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 ...
2
votes
1answer
674 views
Variation in PCA weights
I have weights of SNP variation (output through Eigenstrat program) for each SNP for the three main PCs. I wish to reduce my list of SNPs to those that show maximum differentiation between the three ...
8
votes
3answers
841 views
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 ...
3
votes
1answer
83 views
Approximation of explained variance
I am reading a paper on "multi-SNP" GWAS data analysis method,
The author fitted a linear model $y = \beta_g g + \epsilon$, where $g$ is a genotype vector for a single gene, $\beta_g$ is the true ...
