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

[Benilton Carvalho]

Dear Javier,

You have not provided the exact call to RMA you used nor your  
sessionInfo() information.

If you're using the latest oligo (BioC 2.5), you can call:

results = rma(object, target="core")

to get the 33297 "probesets" you refer to...

Note that building the package yourself is a nice exercise, but you  
could just download it via biocLite().

Cheers,

b

On Oct 29, 2009, at 5:42 PM, Javier Pérez Florido wrote:

> 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.r4.pgf
> HuGene-1_0-st-v1.r4.clf
> HuGene-1_0-st-v1.na29.hg18.probeset (CSV file)
>
> Then, I executed the following commands:
> library(pdInfoBuilder)
> 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??
> Thanks,
> Javier
>
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