05-25-2016 12:01 AM
I tried to run the HWE test using following procedure - And I got the following error
ERROR: There are no individuals with any non-missing genotypes.
One of the my observation has value Undeter instead of AA or GG etc
How can I fix this issue?
proc allele data=SNP393_A outstat=ld prefix=Marker
perms=10000 boot=1000 seed=123 genocol;
05-25-2016 01:27 AM
I'm not familiar with the procedure ALLELE but the error you are getting suggests that your variables g1 to g5 contain only missing values. These variables need to be populated for at least some of your data rows to fix the error.
05-25-2016 01:56 AM
Read the documentation for the PROC ALLELE statement:
indicates that columns specified in the VAR statement contain genotypes instead of alleles. When this option is specified, there is one column per marker. The genotypes must consist of the two alleles separated by a delimiter. For a genotype with one missing allele, use a blank space to indicate a missing value; if both alleles are missing, either use a single missing value for the entire genotype or use the delimiter alone.
(Bold and underline by me)
05-25-2016 02:00 AM