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:
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?