[BioC] Analysing Human Gene ST 1.0 Arrays with oligo and oneChannelGUI yield different number of probesets

Javier Pérez Florido jpflorido at gmail.com
Thu Oct 29 20:42:52 CET 2009

Dear list,
Some time ago I analysed a set of Human Gene ST Arrays with 
oneChannelGUI. Now I'm trying to reproduce the results using oligo 
package but I am quite surprised with the results obtained. With oligo 
package, after preprocessing with rma, the number of probesets are 
253002 while with oneChannelGUI the number of probesets are 33297, and 
the CEL files are the same!!!

For oligo package, and prior to read the CEL files,  I had to build the 
annotation package using pdInfoPackage, since the CDF file is not 
supported by Affymetrix. For this purpose, first I had to download the 
library files "Human Gene 1.0 ST Array, Analysis" from Affymetrix 
website. The necessary files for building the package are:
HuGene-1_0-st-v1.na29.hg18.probeset (CSV file)

Then, I executed the following commands:
baseDir <- "pathWhereTheFilesAre"
(pgf <- list.files(baseDir, pattern = ".pgf",full.names = TRUE))
(clf <- list.files(baseDir, pattern = ".clf",full.names = TRUE))
(prob <- list.files(baseDir, pattern = ".probeset.csv",full.names = TRUE))
seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = 
clf,probeFile = prob, author = "Javier",email = "email",biocViews = 
"AnnotationData",genomebuild = "NCBI Build 36",organism = "Human", 
species = "Homo Sapiens",url = "")
makePdInfoPackage(seed, destDir = ".")

And I installed the package:
R CMD INSTALL pd.hugene.1.0.st.v1\

The package was installed OK and I read and preprocessed the CEL files 
using RMA, but the number of probesets are 253002!!!! So many probesets 
compared to the ones given by oneChannelGUI.

Any comments for such big difference??

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