Scripts to perform meta-analysis of cancer gene expression datasets
Dependencies:
Install the R/Bioconductior dependencies:
pp <- c("Biobase", "BiocGenerics", "org.Hs.eg.db", "survival", "survcomp", "genefu", "mRMRe", "WriteXLS")
source("http://bioconductor.org/biocLite.R")
myrepos <- biocinstallRepos()
rr <- biocLite(pkgs=pp, dependencies=TRUE, type="source", destdir=".")
If using Windows:
- WriteXLS needs Perl to be installed. To check if perl has been installed: library(WriteXLS) testPerl(perl="perl", verbose=TRUE)
TODO
- Adapt the package to handle curatedOvarianData
- Weighted survival does not work properly (number of patients per time points should be "unweighted")