Hi, I have a dataset containing approximately 2 million SNPs. The data is in PLINK format. The data conversion was successful except for a warning message "Nan introduced due to coercion". My problem is that I get an error message when I perform a PCA: "Principal Component Analysis (PCA) on SNP genotypes: Removing 67 non-autosomal SNPs.Error in snpgdsPCA(genofile) : There is no SNP!" Here is my script: #load BED files bed2L<-“/home/2L_hwe_cleaned.bed” bim2L<-“/home/2L_hwe_cleaned.bim” fam2L<-“/home/2L_hwe_cleaned.fam” #convert format snpgdsBED2GDS(bed2L, bim2L, fam2L, “chr2L”) #open filegenofile<-openfn.gds(“chr2L”) #perform pcapca<-snpgdsPCA(genofile) I would appreciate some help. Thanks,Danica [[alternative HTML version deleted]]