conversion from CEL file to PLINK format (.map, .ped)

Question

[more.u88]

Hi! I'm writing this message because I'm not an expert to treat genetical data and since I want to perform an analysis using PLINK software I would like to ask you how I can convert CEL files to the map and ped format that I can use in PLINK. I'm searching online but I'm not understanding. Also, someone could explain me better the structure of CEL files or where I can find some good references to understand better.

Thank you very much

[zx8754]

Relevant post at bioconductor:

• https://support.bioconductor.org/p/30380/

And

• Creation Of Plink Files

Answer 1

[Giulio Genovese]

You can use the affy2vcf bcftools plugin to convert the apt-probeset-genotype output to VCF and then use best practices to convert the VCF output to PLINK. I believe this is the fastest way