The CEL file is the raw data from a microarray experiment, so to retrieve genotype information you will first need to normalise the data and then analyse it. Limma is a good R package for doing this, and there is plenty of documentation available via this website: http://www.bioconductor.org/packages/release/bioc/html/limma.html

I see an answer discussing gene expression. If you do want to extract genotypes from an affymetrix genotyping chip, look at R and bioconductor. Several packages, one is the crlmm package.

Gerard Tromp sir,

   crlmm package is giving  an error

Code for R is :

outdir

How many samples do you have. There seems to be a known error with small sample sizes.

There are 12 .cel files of GSE20986 from Gene Expression Omnibus