Question: Where to obtain case-control GWAS datasets.
1
gravatar for edufoju
5.2 years ago by
edufoju10
Spain
edufoju10 wrote:

Hi!

I've been developing a tool, in R, to GWAS analyze SNP array for affymetrix 5.0 and 6.0.

Now I want to obtain some real data case-control (raw files .CEL) to try my code, and see if it works correctly. Comparing with the real papers and see if we detect the same snps.

Do you know where to obtain this kind of data? I've been searching around and there are no open datasetes. Or if they are they are not complete. For example in GEO db I found the case cohort but there is not uploaded the control cohort.

Thank you!

gwas snp R • 2.3k views
ADD COMMENTlink modified 3.4 years ago by Shicheng Guo7.6k • written 5.2 years ago by edufoju10
3
gravatar for Laura
5.2 years ago by
Laura1.7k
Cambridge UK
Laura1.7k wrote:

You should investigate the data sets you can find in the https://www.ebi.ac.uk/ega/

This is where the majority of the WTCCC data is stored

 

 

ADD COMMENTlink written 5.2 years ago by Laura1.7k
1
gravatar for Shicheng Guo
3.4 years ago by
Shicheng Guo7.6k
Shicheng Guo7.6k wrote:

You can find useful case-control association data from http://www.ncbi.nlm.nih.gov/gap

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Shicheng Guo7.6k
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