[BioC] ExpressionSet Time-series correlation stuff

[Forst, Christian]

Is there an easier way to do time-series correlation between genes of an ExpressionSet other than using for-loops and cor()? especially if I want to play with the particular time-series?
And I am not really happy with the packages I found so far: bioDist, qpgraph, qvalue

I have:

es...ExpressionSet
ts <- c("t1", "t2", "t3", "t4", "t5")  some time series from es (out of many)

sp <- matrix(nrow=10,ncol=10)
for(i in 1:10) {
  sp[i,i] <- 1.
  for(j in i:10) {
    sp[i,j] <- cor(as.vector(exprs(es[i,ts])), as.vector(exprs(es[j,ts])), method="spearman")
    sp[j,i] <- sp[i,j]
  }
}

And I actually want to do this for all the 40000 genes in es and not 10 as given in the example.

Thanks - Chris