R (>= 3.0.0), shiny (>= 0.8.0), WGCNA, igraph, shinyBS, RColorBrewer, Hmisc, psych, RJSONIO, whisker, yaml, pheatmap, preprocessCore, GO.db, AnnotationDbi, impute, and ggplot2
$ source("http://bioconductor.org/biocLite.R")
$ biocLite("impute")
$ biocLite("preprocessCore")
$ biocLite("GO.db")
$ biocLite("AnnotationDbi")
$ install.packages(c("WGCNA", "igraph", "RColorBrewer", "Hmisc", "psych",
"RJSONIO", "whisker", "yaml", "pheatmap", "ggplot2"))
Please, install versions 0.8.0 and 0.20 for shiny and shinyBS, respectively.
We are working to make the CoGA package compatible with the new versions of the packages as soon as possible. To install the recommended versions for shiny and shinyBS, just type the following commands on the R command-line:
$ install.packages("devtools")
$ devtools::install_version("shiny", "0.8.0")
$ devtools::install_version("shinyBS", "0.20")
$ install.packages(path_of_the_downloaded_file)
For example, if you use Linux and save the CoGA package at your Desktop, you would probably do:
install.packages("~/Desktop/coga_0.01-1.tar.gz")
library(coga)runCoga()
REMBRANDT_ODII_AII_log2_normalized_data.txt
We have downloaded raw CEL files from 65 astrocytoma grade II
and 30 oligodendroglioma grade II microarrays at the REMBRANDT
portal (
https://caintegrator.nci.nih.gov/rembrandt), and then used the
justRMA
function from the affy
package
(
http://www.bioconductor.org/packages/release/bioc/html/affy.html)
to pre-process them. To group probes into probe sets, we have used
the Brain array custom CDF file (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), ENTREZG v. 18.0.0.0.
No annotation data is required in this example. If you need to collapse your dataset to gene symbols, you can download CHIP files from the Broad ftp site (ftp://gseaftp.broadinstitute.org/pub/gsea/annotations).
In this file, "AII" means astrocytoma grade II, and "ODII" means oligodendroglioma grade II.
Before running CoGA, you must enter a collection of gene sets.
You can find several collections of gene sets in gmt format freely available at the Molecular Signature Database (MSigDB) (http://www.broadinstitute.org/gsea/msigdb/collections.jsp).