I am analyzing the GSE27157 dataset using the raw CEL files. I want to use custom cdf "HGU133PLUS2_HS_ENTREZG". I downloaded the cdf file "GPL23270_HGU133Plus2_Hs_ENTREZG.cdf.gz" from here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL23270. This is the script that I tried:
celfiles <- read.affy(covdesc="phenodata.txt", path="data", cdfname="HGU133PLUS2_HS_ENTREZG")
However, I got this error:
Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HGU133PLUS2_HS_ENTREZG Library - package hgu133plus2hsentrezgcdf not installed Bioconductor - hgu133plus2hsentrezgcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)
I tried to install package hgu133plus2hsentrezgcdf , but I received this error:
BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). Installing package(s) ‘hgu133plus2hsentrezgcdf’ installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, survival Warning message: package ‘hgu133plus2hsentrezgcdf’ is not available (for R version 3.3.2)
Any help is greatly appreciated!!