SNP data anlaysis

Question

[496527]

Hello ~

I try to make breast cancer case and control dataset to analyze in Plink.

I don't have any dataset like WTCCC

so I try to make dataset using GEO.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19594

to make plink .ped and .map file I don't know how to process these dataset.

Please help me~

Thank you so much!

[WouterDeCoster]

What have you tried?

[Medhat]

there is two copies from the same question am I right?
SNP data anlaysis
SNP data anlaysis

[WouterDeCoster]

Right, I closed the other one.

[Denise CS]

What are you exactly trying to achieve? Do you have new data from patients with breast cancer? There is lot of GWAS data out there for this disease, including linking the results of associations by lead SNPs to genes for drug discovery (e.g. 165 targets associated with breast carcinoma based on the data from the GWAS catalog only).

Answer 1

[496527]

I downloaded an make data like this (using R)

row is sample and column is SNP (but SNP numbers and row numbers aren't same- I don't know why) and every attribute is AA/AB/NoCall like that.

Thank you so much~