intcor: Integrative Correlation Analysis

In metaArray: Integration of Microarray Data for Meta-analysis

Description

This function calculates gene-specific reproducibility score based on Parmigiani et al. R implementation in MergeMaid (pairwise.cor) is a very efficient function in that it calculates the correlation matrix only once and collect appropriate elements for calculation of scores for each gene. However, in case there are more than thousands of common genes across datasets, the correlation matrix may overflow memory cells alloted to a session of R. Therefore, a replacement to the function that remedies the storage problem by brute force but fast computation in C is provided here.

Usage

  intcor(merged)

Arguments

merged

mergeExprSet object that contains gene expression and class label with all datasets.

Value

avg.cor	A vector of gene-specific integrative correlation score
pair.cor	A matrix of correlations for each gene in every pair of two studies

Author(s)

Debashis Ghosh <[e-mail]>, Hyungwon Choi <[e-mail]>

References

Clinical Cancer Research, Parmigiani et al. 10(9):2922-2927, 2004

Examples

 #intcor(merged)

metaArray documentation built on April 29, 2020, 2:12 a.m.