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 >...... -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero