Detection of global group effect

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Description

Tests a global effect for a set of molecular features (e.g. genes, proteins,...) between the two groups of samples. Missing values are allowd in the expression data. Samples of the two groups are supposed to be unpaired.

Usage

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  GlobTestMissing(X1, X2, nperm = 100)

Arguments

X1

Matrix of expression levels in first group. Rows represent features, columns represent samples.

X2

Matrix of expression levels in second group. Rows represent features, columns represent samples.

nperm

Number of permutations.

Value

The p-value of a permutation test.

Author(s)

Klaus Jung Klaus.Jung@ams.med.uni-goettingen.de

Examples

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### Global comparison of a set of 100 proteins between two experimental groups,
### where (tau * 100) percent of expression levels are missing.
n1 = 10
n2 = 10
d = 100
tau = 0.1
X1 = t(matrix(rnorm(n1*d, 0, 1), n1, d))
X2 = t(matrix(rnorm(n2*d, 0.1, 1), n2, d))
X1[sample(1:(n1*d), tau * (n1*d))] = NA
X2[sample(1:(n2*d), tau * (n2*d))] = NA
GlobTestMissing(X1, X2, nperm=100)