Displaying 2 results from an estimated 2 matches for "expressionlevel".
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expression_level
2011 Oct 30
1
Normality tests on groups of rows in a data frame, grouped based on content in other columns
Dear R users,
I have a data frame in the form below, on which I would like to make normality tests on the values in the ExpressionLevel column.
> head(df)
ID Plant Tissue Gene ExpressionLevel
1 1 p1 t1 g1 366.53
2 2 p1 t1 g2 0.57
3 3 p1 t1 g3 11.81
4 4 p1 t2 g1 498.43
5 5 p1 t2 g2 2.14
6 6 p1 t2 g3 7.85
I would like to make the tests on every gr...
2011 Mar 02
0
Selecting a subsample so that it follows a distribution.
...n.
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(!is.na(match(geneSet[,1],geneExp[index,1])))
}...