How to use Brainarray CDF for gcrma?

Question

[oolongoni]

Hello,

I am trying to analyze the GSE24759 dataset using the raw CEL files. I was hoping to use gcrma to process the data but ran into complications downloading the custom CDF "U133AAofAv2_Hs_ENTREZG" from Brainarray. http://brainarray.mbni.med.umich.edu/bioc/ I found a tutorial here (https://github.com/obigriffith/biostar-tutorials/blob/master/MachineLearning/processAffyTestData.R) which is very helpful. I copied the links to the R Source Packages.

# install R Source Packages from 
# http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/entrezg.asp

> library(devtools)
> install_url("http://mbni.org/customcdf/21.0.0/entrezg.download/u133aaofav2hsentrezgcdf_21.0.0.tar.gz")
> install_url("http://mbni.org/customcdf/21.0.0/entrezg.download/u133aaofav2hsentrezgprobe_21.0.0.tar.gz")
> install_url("http://mbni.org/customcdf/21.0.0/entrezg.download/pd.u133aaofav2.hs.entrezg_21.0.0.tar.gz")
> install_url("http://mbni.org/customcdf/21.0.0/entrezg.download/u133aaofav2hsentrezg.db_21.0.0.tar.gz")

# load the libraries
> library(u133aaofav2hsentrezgcdf)
> library(u133aaofav2hsentrezgprobe)
> library(u133aaofav2hsentrezg.db)
> library(u133aaofav2hsentrezg.db)

# read in CEL files
> cels = list.files("data/", pattern = "CEL")
> raw.data = ReadAffy(verbose=TRUE, filenames=cels, cdfname="u133aaofav2hsentrezgcdf")
> gcrma.data=gcrma(raw.data)
Adjusting for optical effect............................................................ ....................................................................................... ................................................................Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment u133aaofav2hsentrezgcdfcdf was not found in the Bioconductor repository."
[1] "Checking to see if your internet connection works..."
[1] "Environment u133aaofav2hsentrezgcdfprobe was not found in the Bioconductor repository."
Error in get(probepackagename) : 
  object 'u133aaofav2hsentrezgcdfprobe' not found

What is the problem here? I've searched the Bioconductor and Biostar forums but simply cannot figure this out. Any help is greatly appreciated!

Answer 1

[oolongoni]

Solved it! It was erroneously naming the cdfname. Doh!

raw.data = ReadAffy(verbose=TRUE, filenames=cels, cdfname="u133aaofav2hsentrezg") ## not "u133aaofav2hsentrezgcdf"

Answer 2

[sinnamone]

This is not correct:

load the libraries

library(u133aaofav2hsentrezgcdf) library(u133aaofav2hsentrezgprobe) library(u133aaofav2hsentrezg.db) library(u133aaofav2hsentrezg.db)

but you should write

load the libraries

library(u133aaofav2hsentrezgcdf) library(u133aaofav2hsentrezgprobe) library(pd.u133aaofav2.hs.entrezg_21) library(u133aaofav2hsentrezg.db)