PCA scores when using *.bed, *.bim, *.fam files

[namheegordonkim]

Suppose we have the following files:
in.bed, in.bim, in.fam

The command:

smartpca.perl -i in.bed -a in.bim -b in.fam -s 6 \
-e out.eval -l out.elog -o out.pca -p out.plot

results in out.pca having only zero entries. On the other hand, using plink to recode the binary files into *.ped and *.map, the commands:

smartpca.perl -i in.ped -a in.map -b in.ped -s 6 \
-e out.eval -l out.elog -o out.pca -p out.plot

and

smartpca.perl -i in.ped -a in.map -b in.fam -s 6 \
-e out.eval -l out.elog -o out.pca -p out.plot

both compute the same eigenvalues as the previous one, but the PCA scores are correctly computed.