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= RでNMF(Nonnegative Matrix Factorization)パッケージをインストール

[2012-12-21 14:49:40]

潜在変数を探したいというか,行列分解をしてみたくてNMFを使おうと思ったが,
CRANからはRのパッケージが削除されてたらしい.

Package ‘NMF’ was removed from the CRAN repository.

CRAN - Package NMF

というわけで,CRAN-like repository <Renaud Gaujoux>を参考に,

> install.packages('NMF', repos=c('http://web.cbio.uct.ac.za/~renaud/CRAN', getOption('repos')))
(略)
> library(NMF)
Loading required package: pkgmaker
Loading required package: rngtools
Loading required package: registry
Loading required package: digest
Loading required package: grid
NMF - Loading BioConductor layer ... NO [missing Biobase]
  To enable, try: install.extras('NMF') [with Bioconductor repository enabled]
NMF - Checking shared memory capabilities ... NO [missing bigmemory]
  To enable, try: install.extras('NMF')
> install.extras('NMF', repos=c('http://web.cbio.uct.ac.za/~renaud/CRAN', getOption('repos')))
(略)
Loading required package: Biobase
Warning messages:
1: package ‘Biobase’ is not available (for R version 2.15.2) 
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
> library(NMF)
> example(NMF)

Biobaseがないって警告出てるけど,NMFは読み込めたみたい.

source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")

Bioconductor - Biobase

これをあらかじめ実行しておけばBiobaseもインストールできる


マニュアルはここ(PDF)か,私の環境では

/Users/peccu/R/x86_64-apple-darwin12.2.0-library/2.15/NMF/doc/NMF-vignette.pdf

にありました.