How to: Create a CDF file from Bioconductor Platform Design (PD) Info package

Author: Mark Robinson and Henrik Bengtsson with contributions from Samuel Wuest.
Created on: 2009-01-15
Last updated: 2012-12-06

Below is an example session for converting the pd.hugene.1.0.st.v1 package (i.e. for the HuGene-1_0-st-v1 chip type) created using the pdInfoBuilder package (to create such a package from scratch, see section at the end). The following commands will build a CDF file, which you can deposit in the correct directory to use with aroma.affymetrix:

library("aroma.affymetrix")
library("pd.hugene.1.0.st.v1")
pathname <- writeCdf(pd.hugene.1.0.st.v1, tags="pd.hugene.1.0.st.v1,HB20110111", overwrite=TRUE)
print(pathname)
## [1] annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf

You can verify this CDF file against the CDF file you can download from the HuGene-1_0-st-v1 page.

Creating a Package Design Info (PD) package from Affymetrix annotation files

To create an R package using pdInfoBuilder in the first place, you need to download the library files, probe.tab files, and NetAffx Annotation files from Affymetrix (Human Gene 1.0 ST). Then use the commands:

library("pdInfoBuilder")
chipType <- "HuGene-1_0-st-v1"
pgfFile <- sprintf("%s.r3.pgf", chipType)
clfFile <- sprintf("%s.r3.clf", chipType)
probeFile <- sprintf("%s.probe.tab", chipType)
transFile <- sprintf("%s.na27.hg18.transcript.csv", chipType)
pkg <- new("AffyGenePDInfoPkgSeed",
          version="0.0.1",
          author="Mark Robinson", email="mrobinson@...",
          biocViews="AnnotationData",
          genomebuild="hg18",
          pgfFile=pgfFile, clfFile=clfFile,
          probeFile=probeFile, transFile=transFile)
makePdInfoPackage(pkg, destDir=".")

Don't forget to install the PD package afterward, i.e. install.packages("pd.hugene.1.0.st.v1.tar.gz", repos=NULL).