Question: How to use custom cdf "hgu133plus2hsentrezgcdf"?
3
22 months ago by
rahil30
rahil30 wrote:

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
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!!

modified 22 months ago • written 22 months ago by rahil30
Answer: How to use custom cdf "hgu133plus2hsentrezgcdf"?
2
22 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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/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).

Many thanks Guido, it is really helpful.

Answer: How to use custom cdf "hgu133plus2hsentrezgcdf"?
0
22 months ago by
rahil30
rahil30 wrote:

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

The error is a little cryptic, but with a bit of thought it should have been pretty clear. It says, in part,

hgu133plus2hsentrezg.db package not attached

which technically should be

hgu133plus2hsentrezg.db package is not loaded

and you use the library function to load a package, and for R to use a package it has to be loaded first. So if you have installed the package, load it. If it isn't installed, then install it and then load it.