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.corA vector of gene-specific integrative correlation score
pair.corA matrix of correlations for each gene in every pair of two studies
References
Clinical Cancer Research, Parmigiani et al. 10(9):2922-2927, 2004