Hello,

I am creating a cluster file to use in plink for stratified analyses/breslow-day tests/ homogeneity tests. I read on the plink website that: This file should have a similar structure to the alternate phenotype file. The clusters can be coded either numerically or as strings:

F1 I1  A
F2 I1  B
F3 I1  B
F4 I1  C1
F5 I1  A
F6 I1  C2
F7 I1  C2
 ...

Here, individuals would be grouped in four groups:

Cluster A:  F1/I1  F5/I1
Cluster B:  F2/I1  F3/I1
Cluster C1: F4/I1  
Cluster C2: F6/I1  F7/I1
...

All individuals in the file should be assigned to a single cluster in the cluster file.

This is all fine. Except this last statement. What if my control set stays the same within each strata.

Example: Age1 vs. entire control set = Cluster A

Age2 vs. entire control set = Cluster B

Age 3 vs. entire control set = Cluster C

Meaning this control set is in each cluster- but I can only assigned an individual to 1 cluster..

Has anyone else had this problem? Any suggestions? Thank you.