Hi dear all,

I am handling my first iScan SNP genotype data, my data is the MEGA chip bead-level data. I success accessing quality, but I don't know how to normalize and call the genotype.

The crlmm package can be used to analyse the SNP genotyping If I get the idat format file. But I didn't find the corresponding annotation file to the MEGA chip.

Are there any other packages to handle my MEGA snp data?

Can you give me some suggestion?  You help is greatly appreciated.

Ting Hou