XDE (version 2.18.0)

xsScores: Alternative cross-study scores of differential expression

Description

Alternative cross-study scores of differential expression

Usage

xsScores(statistic, N)

Arguments

statistic

a matrix of study-specific estimates of effect size. Rows are genes and columns are studies.

N

numerical vector: the number of samples in each study (the length should be the number of columns in statistic)

Value

A matrix of cross-study scores for differential expression ("diffExpressed"), concordant differential expression, and discordant differential expression.

References

J.K. Choi, U. Yu, S. Kim, and O.J. Yoo (2003), Combining multiple microarray studies and modeling interstudy variation, Bioinformatics, 19(1) I84-I90.

E. Garrett-Mayer, G. Parmigiani, X. Zhong, L. Cope, and E. Gabrielson (2007), Cross-study validation and combined analysis of gene expression microarray data, Biostatistics, September

R. Scharpf et al., A Bayesian Model for Cross-Study Differential Gene Expression, Technical Report 158, Johns Hopkins University, Department of Biostatistics, 2007

See Also

the GeneMeta package, ssStatistic

Examples

  data(expressionSetList)
  t <- ssStatistic(statistic="t", phenotypeLabel="adenoVsquamous", esetList=expressionSetList)
  tScores <- xsScores(t, N=nSamples(expressionSetList))