Hi there, I have a problem with adding another chip specs. to my libraries. Based on the CEL -> Cibersort conversion script, I ran
as root to install the chip specs, but when I run
source("http://bioconductor.org/biocLite.R") library(affy) library(annotate) library(hgu133plus2hsentrezgcdf) library(org.Hs.eg.db) library('hthgu133pluspmprobe') allFiles <- list.files('./GSE45291',full.names=TRUE) Data<-ReadAffy(filenames = allFiles[0:10],cdfname = "hthgu133pluspmprobe") #eset<-rma(Data) eset<-mas5(Data)
mas5 gives me
background correction: mas PM/MM correction : mas expression values: mas background correcting... Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hthgu133pluspmprobe Library - package hthgu133pluspmprobecdf not installed Bioconductor - hthgu133pluspmprobecdf not available
What am I doing wrong? It worked before for some reason. Sorry, but I am relatively new to Bioconductor and R, I am a C++ person.