Hi all,

I have some genotype datasets from Illumina and Affymetrix, I am a bit confused because I still have an abnormal pca plot after merging the data using --bmerge with plink. They are in ATGC allele.

What I did: get the Pan Asian dataset (Affymetrix 50k_Xba Gene chip), recode the 0,1,2,9 allele to ATGC, get a 1000 genome dataset from Discovery blog (Illumina ~50k SNP) in ATGC allele, a dataset from my project (Illumina humanomniexpress 24 v1.1a 1M SNP) in ATGC allele. I removed missing genotype in the data using --geno, merge the two datasets after resolving the strand issue using --flip and --bmerge.

I am supposed to get African and Southeast Asian populations in both side of my sample populations but it is not the case. and I think it might be a platforms merging issue.

Thank you for your help