R version 2.13.2 (2011-09-30)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)

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[Previously saved workspace restored]

> setwd("C:/Users/S. BHUPINDER SINGH/Desktop/2nd Co-op term/BC Cancer Research Centre/Work/Jeremy Tasks/Martin/GAGE/Gage_run_11_Jan_2012")
> getwd()
[1] "C:/Users/S. BHUPINDER SINGH/Desktop/2nd Co-op term/BC Cancer Research Centre/Work/Jeremy Tasks/Martin/GAGE/Gage_run_11_Jan_2012"
> ### R code from vignette source 'vignettes/gage/inst/doc/gage.Rnw'
> 
> ###################################################
> ### code chunk number 1: install (eval = FALSE)
> ###################################################
> ## source("http://bioconductor.org/biocLite.R")
> ## biocLite(c("gage","gageData"))
> 
> 
> ###################################################
> ### code chunk number 2: install (eval = FALSE)
> ###################################################
> ## install.packages(c("/your/local/directory/gage_2.0.0.tar.gz",
> ##     "/your/local/directory/gageData_1.0.0.tar.gz"), 
> ##     repos = NULL, type = "source")
> 
> 
> ###################################################
> ### code chunk number 3: start
> ###################################################
> options(width=80)
> 
> 
> ###################################################
> ### code chunk number 4: start
> ###################################################
> library(gage)
Loading required package: graph
Loading required package: multtest
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Warning message:
'.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated") 
> 
> 
> ###################################################
> ### code chunk number 5: start (eval = FALSE)
> ###################################################
> ## library(help=gage)
> 
> 
> ###################################################
> ### code chunk number 6: start (eval = FALSE)
> ###################################################
> ## help(gage)
> ## ?gage
> 
> 
> ###################################################
> ### code chunk number 7: dataPrep
> ###################################################
> Micro_array_dataset <- read.table("Micro_array_dataset.txt")
> cn=colnames(Micro_array_dataset)
> hn=grep('HN',cn, ignore.case =T)
> adh=grep('ADH',cn, ignore.case =T)
> dcis=grep('DCIS',cn, ignore.case =T)
> print(hn)
integer(0)
> print(dcis)
integer(0)
> 
> 
> ###################################################
> ### code chunk number 8: dataPrep
> ###################################################
> Gene_set <- read.table("Gene_set.txt")
> #data(kegg.gs)
> #data(go.gs)
> lapply(Gene_set[1:3],head)
Error in `[.data.frame`(Gene_set, 1:3) : undefined columns selected
> head(rownames(Micro_array_dataset))
[1] "ENSG00000000003" "ENSG00000000005" "ENSG00000000419" "ENSG00000000457"
[5] "ENSG00000000460" "ENSG00000000938"
>