无法在R中加载Bioconductor程序包基因组范围的np6cdf

时间:2018-11-14 19:25:44

标签: r bioconductor

R和Bioconductor的新手,我正在研究从别人那里得到的代码。我这样做:

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

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("affy", version = "3.8")
BiocManager::install("oligo", version = "3.8")
BiocManager::install("pd.genomewidesnp.6", version = "3.8")

library(Biobase)
library(affy)
library(oligo)
library(pd.genomewidesnp.6)

data <- ReadAffy('myfile.CEL')

'myfile.CEL'是来自Synapse中特定项目的69 MB .CEL文件。这是data加载到我的环境中后的样子: enter image description here

然后如果我eset <- rma(data)出现错误:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’

如果我这样做eset <- affy::rma(data),我会得到:

Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain GenomeWideSNP_6
Library - package genomewidesnp6cdf not installed
Bioconductor - genomewidesnp6cdf not available

Google搜索没有告诉我genomewidesnp6cdf是什么,它是否与pd.genomewidesnp.6相同,以及为什么我没有它。有人知道吗?

0 个答案:

没有答案