Closed nm15336 closed 12 months ago
Hey, so I have this error when running step 1 of saige with a subset of my plink files, and pheno file:: saige1-out.txt
5685 samples in geno file do not have phenotypes 0 samples will be used for analysis
But as confirmed in R, there is large overlap between these files and should be around ~3000 samples. saige-intersection.txt
Please see full attached .out file for the full error, and the R file which shows there is overlap
Is there another reason I could be getting this error / the ID isn't parsing correctly between the files when using saige?
Thanks!
P.S error remains the same when I dos2unix, keep only one fid/iid column, remove missing data, or use a different phenotype
Hey, so I have this error when running step 1 of saige with a subset of my plink files, and pheno file:: saige1-out.txt
5685 samples in geno file do not have phenotypes 0 samples will be used for analysis
But as confirmed in R, there is large overlap between these files and should be around ~3000 samples. saige-intersection.txt
Please see full attached .out file for the full error, and the R file which shows there is overlap
Is there another reason I could be getting this error / the ID isn't parsing correctly between the files when using saige?
Thanks!
P.S error remains the same when I dos2unix, keep only one fid/iid column, remove missing data, or use a different phenotype