I am trying to learn statistical methods in bioinformatics. Given 2 datasets, a gene expression dataset containing a set of genes from many individuals in a 500 by 10 matrix form and the other containing genotypes in 500 by 5 matrix. If we're to find how the genes and genotypes are associated, first I'd like to understand the genotype dataset. A snapshot of it looks like below:
0 2 1 1 1
0 0 2 1 2
2 0 1 1 2
0 2 2 1 2
2 0 1 1 1
How to understand the above dataset and how does it relate to the gene expression dataset ?
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kapali •
These genotypes look like they're encoded:
Thank you!Could you also please guide me as to how to relate both of these matrices. A row of the gene expression data looks such:
7.86490091464696 8.1723619701534 8.34552212860064 9.41797297608165 7.36968490544839 9.39360171067621 7.64949009855557 10.2651072819383 9.35328948474585 8.84157842635477 (for 10 genes in one individual).
Supposing we are to find gene-SNP pairs that are related, how to do so?
It's hard to tell by just giving me a row of numbers, but my guess is that these are normalized expression values for 10 genes - if this is from RNA-seq than these are normalized read counts.
Looks like you want to perform an eQTL analysis: looking for SNPs which influence the expression of a (nearby) gene. You may want to read some literature about that or look up some common tools.
Thank you.I found some useful links for doing eQTL analysis eQTL Analysis However in my case, the gene expression matrix is a 500 by 10 matrix (500 persons and 10 genes) and the genotypes matrix is only a 500 by 5 matrix. Most examples on eQTL analysis consider both matrices with the same dimensions. I am wondering how to perform this analysis if dimensions of the above 2 matrices are different.
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