Questions tagged [snp-chip]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0
votes
1answer
20 views

Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?

I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
1
vote
1answer
27 views

Convert SNP data from GEO into PED and MAP files?

I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147 GEO provides data as SOFT ...
4
votes
1answer
86 views

Statistical approach to compare the SNP genotyping data among set of individuals

So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. ...
4
votes
1answer
92 views

Compute copy number from cases and controls

I have some data on Copy Number Variation (SNP chip) for a population of samples. In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another ...