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Forst, Christian
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@forst-christian-5709
Last seen 7.7 years ago

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