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

[Javier Pérez Florido]

Dear Benilton,
Thanks for your quick reply. Now, it works with the target argument. 
However, I searched on the web for the meaning of this argument and 
couldn't find anything. What is "target" for?
Why does oligo's manual say: "The ExpressionSet returned when either 
Exon/Gene-FeatureSet objects are passed contain extra annotation on the 
featureData slot that the user should take into account for
exon/gene-level analyses"?
I didn't work with Human Gene ST arrays before, so, I quite new on this 
topic.
Thanks again,
Javier





Benilton Carvalho escribió:
> 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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>
>