Hello,

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!!

The remapped, custom CDFs can not be downloaded using BiocLite(); you rather have to download them directly from the MBNI group website.

As an example, assuming you are on windows and would like to use the latest version (=v22) of the custom CDFs:

install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133plus2hsentrezgcdf_22.0.0.zip")
install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133plus2hsentrezgprobe_22.0.0.zip")
install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133plus2hsentrezg.db_22.0.0.zip")

Also, when using the function read.affy you should change the argument cdfname into cdfname='hgu133plus2hsentrezg'.

<<edit>> I just noticed that at GEO it is stated that v21 of the custom CDF was used (and not v22 [latest]). To download that version, please replace the number '22' by '21' in the links above (i.e. 2x replacement per link). 

what's the problem here? When I try to get the symbols for my probe set list after deferentially gene expression analysis by limma.

probeset.list <- topTable(dge, coef=1, number=100, lfc=2)
gene.symbols <- getSYMBOL(rownames(probeset.list), "hgu133plus2hsentrezg")

I got this error:

Error: getAnnMap: hgu133plus2hsentrezg.db package not attached and load is FALSE

Thanks for your help!