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basechan
2011 Mar 02
0
Selecting a subsample so that it follows a distribution.
...llow the same expression level distribution.
This is what I've done so far:
geneExp is my data.frame with DE statistics. 6585 rows of genes, col one is
gene ID.
geneSet is my gene set, column one is gene ID.
index is the index of the genes DE in my geneExp.
dSign=density(geneExp[index,'baseMean']) #baseMean is a measure of
expressionlevel
prob=lapply(geneExp[,"baseMean"],function(x) approx(dSign$x,dSign$y,x)$y)
prob=unlist(prob)
So when I am doing my permutation I do:
overlap=vector(0,length=10000)
for (i in 1:10000) {
index=sample(1:6585,543,prob=prob)
overlap[i]=sum(...