The first 3dANOVA syntax in the message above was confused as we had not finished changing the terminology to make it more comprehensible, so here is a revised version of it:
3dANOVA3 \
-type 5 \
-alevels 2 -blevels 2 -clevels 3 \
-dset 1 1 1 ../../ctrl1/analysis/NegvPosRun1+tlrc'[0]' \
-dset 1 1 2 ../../ctrl2/analysis/NegvPosRun1+tlrc'[0]' \
-dset 1 1 3 ../../ctrl3/analysis/NegvPosRun1+tlrc'[0]' \
-dset 1 2 1 ../../ctrl1/analysis/NegvPosRun2+tlrc'[0]' \
-dset 1 2 2 ../../ctrl2/analysis/NegvPosRun2+tlrc'[0]' \
-dset 1 2 3 ../../ctrl3/analysis/NegvPosRun2+tlrc'[0]' \
-dset 2 1 1 ../../patient1/analysis/NegvPosRun1+tlrc'[0]' \
-dset 2 1 2 ../../patient2/analysis/NegvPosRun1+tlrc'[0]' \
-dset 2 1 3 ../../patient3/analysis/NegvPosRun1+tlrc'[0]' \
-dset 2 2 1 ../../patient1/analysis/NegvPosRun2+tlrc'[0]' \
-dset 2 2 2 ../../patient2/analysis/NegvPosRun2+tlrc'[0]' \
-dset 2 2 3 ../../patient3/analysis/NegvPosRun2+tlrc'[0]' \
-diskspace \
-fa GrpEff \
-fb RunEff \
-fab GrpxRun \
-amean 1 ctrl \
-amean 2 patient\
-bmean 1 run1 \
-bmean 2 run2 \
-bucket ANOVA_SRET_NegvPos
Philippe & Wiveka