Dear Virginia, I am the maintainer of oneChannelGUI. oneChannelGUI summarize intensities using APT tools. One of the important points, indicated in the installation instructions, is that R folder and your data folder are without "space in the path", which are creating problems when the command for APT tool is executed by oneChannelGUI. Please check if you have space in the above indicated paths and be sure that the working folder of oneChannelGUI is the one where the cel files are located. If you are still having troubles please load oneChannelGUI and execute in the main R windows the following commands and send their output to me together with you target file: affylmGUIenvironment$libDirLocation affylmGUIenvironment$aptDir getwd() dir() Cheers Raffaele Message: 13 Date: Sun, 29 Aug 2010 01:21:00 +0200 From:ifig319 at ifi.csic.es To:bioconductor at stat.math.ethz.ch Subject: [BioC] annotations of Human Gene 1.0 ST microarray and oneChannelGUI Message-ID:<20100829012100.lxz5k9x2i7koscgs at webmail.csic.es> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear list, This is my first experience working on microarray data. I am trying to analyze Human Gene 1.0 ST microarray data with oneChannelGUI. However, this seems to be not a straightforward task. I have been playing around with data and the application and I am a little bit confused and without any result yet! First, I installed all the packages and then, followed the user guide instructions. When I select "GENE 1.0 ST ARRAYS: probe sets summary from Affymetrix APT" option to perform a new analysis, it asks me if I want to use APT for gene/exon summaries. I click "yes" and chose the organisms (in my case, Hs). Next, I select the working directory, the target file and answer "no" to the question "are you using genechips version 1.1?". Finally, as APT tool intensity summary option, I select "rma-sketch". Inmmediatly, I get a series of error messages (see below). I really do not know what is happening here. I would like to make the background correction, normalization and summarization, and also run limma. On the other hand, I can load a normalized tab delimited data set and apply some functions on it, but I do not know how to include the annotations into the final list of differential expressed genes (top table). anybody has a suggestion about what is happening here and how could I solve it? I would appreciate your help. Best regards and thank you in advance for your attention. Virginia. ------- R CONSOLE: Gene level probe sets summary started Gene level probe sets summary ended Error en as.matrix(my.exons) : ninguna funci?n desde donde volver, saltando a nivel superior Adem?s: Mensajes de aviso perdidos 1: In file(file, "rt") : s?lo fue usado el primer elemento del argumento 'description' 2: In system(gene.rma.sketch, wait = T) : C:/Archivos no encontrado 3: In file(file, "rt") : no fue posible abrir el archivo 'C:/onChannelGUI/out5f906952/': No such file or directory -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0116706487 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it