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

[rcaloger]

Dear Javier,
oneChannelGUI uses apt tools for intensity summarization. In version 2.4 of Bioconductor gene-level expression
was calculated using HuGene-1_0-st-v1.r3.mps file. In version 2.5 of Bioconductor it uses 
HuGene-1_0-st-v1.r4.mps
Cheers
Raffaele 

>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!!!
> truncated
>......

 

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Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
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Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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