planned comparisons

Hi Nicola,
you told me it's data on selection experiments. Are the data rally three blocks, meaning crosses between selection lines started from three different base populations?

If you write it like this:
model<-aov(egg~block+block:cross)
there there are no main effects for cross, and you only want to compare crosses within blocks. That means that you only want contrasts between different groups in the same block.

To compare these groups, first look at the coefficients of the model, and what they represent.
Reformulating the model like this probably makes comparisons easier:
model<-aov(egg~block:cross)
because all estimates are means per level.

With four crosses per block, are the coefficients of block 1, the first four coefficients in the model?
Say, you want to make simultaneous confidence intervals for all pairwise comparisons for this block:

# contrast matrix

cmatrix<-matrix(rep(0,6*4),nrow=6)
cmatrix[1,1]<-1;cmatrix[1,2]<--1;
cmatrix[2,1]<-1;cmatrix[2,3]<--1;
cmatrix[3,1]<-1;cmatrix[3,4]<--1;
cmatrix[4,2]<-1;cmatrix[4,3]<--1;
cmatrix[5,2]<-1;cmatrix[5,4]<--1;
cmatrix[6,3]<-1;cmatrix[6,4]<--1;

cmatrix

# when this matrix is multiplied with the vector of coefficients,
# every element of the result, is an estimated difference between two means.

# library(multcomp)

# psubset selects the parameters of the block you want to investigate.

simint(model,psubset=1:4,cmatrix=cmatrix)

You should probably make a contrast matrix for all 18 pairwise comparisons simultaneously.

cmatrix<-matrix(rep(0,3*6*4*3),nrow=3*6)
cmatrix[1,1]<-1;cmatrix[1,2]<--1;
cmatrix[2,1]<-1;cmatrix[2,3]<--1;
cmatrix[3,1]<-1;cmatrix[3,4]<--1;
cmatrix[4,2]<-1;cmatrix[4,3]<--1;
cmatrix[5,2]<-1;cmatrix[5,4]<--1;
cmatrix[6,3]<-1;cmatrix[6,4]<--1;

cmatrix[7,5]<-1;cmatrix[7,6]<--1;
cmatrix[8,5]<-1;cmatrix[8,7]<--1;
cmatrix[9,5]<-1;cmatrix[9,8]<--1;
cmatrix[10,6]<-1;cmatrix[10,7]<--1;
cmatrix[11,6]<-1;cmatrix[11,8]<--1;
cmatrix[12,7]<-1;cmatrix[12,8]<--1;

cmatrix[13,9]<-1;cmatrix[13,10]<--1;
cmatrix[14,9]<-1;cmatrix[14,11]<--1;
cmatrix[15,9]<-1;cmatrix[15,12]<--1;
cmatrix[16,10]<-1;cmatrix[16,11]<--1;
cmatrix[17,10]<-1;cmatrix[17,12]<--1;
cmatrix[18,11]<-1;cmatrix[18,12]<--1;

simint(model,psubset=1:12,cmatrix=cmatrix)