Hi, I'm a grad student at Johns Hopkins Univ. We are trying to analyze our affymetrix Exon Array 1.0 data using affylmGUI. But it seems bioconductor does not have the CDF file for this array. Do you have any advice for me? Information of this microarray: http://www.affymetrix.com/products_services/arrays/specific/mouse_exon .affx#1_4 Thanks a lot! -Junjie -- ____________________________________________ Junjie U. Guo, Graduate Student The Solomon H. Snyder Department of Neuroscience The Johns Hopkins University School of Medicine 733 N. Broadway, BRB 706 Institute for Cell Engineering - NeuroICE Hongjun Song Laboratory Baltimore, MD 21205 guojj@jhmi.edu [[alternative HTML version deleted]]

On Wed, Apr 8, 2009 at 6:14 PM, Junjie Guo <guojj@jhmi.edu> wrote: > Hi, I'm a grad student at Johns Hopkins Univ. We are trying to analyze our > affymetrix Exon Array 1.0 data using affylmGUI. But it seems bioconductor > does not have the CDF file for this array. Do you have any advice for me? > > Information of this microarray: > > > http://www.affymetrix.com/products_services/arrays/specific/mouse_ex on.affx#1_4 > Hi, Junjie. I do not think that affylmGUI will handle the exon arrays (someone will correct me if I am wrong, I am sure). You'll need to use something other than the affy package. See here for details: http://bioconductor.org/docs/workflows/oligoarrays/ There is not a GUI for any of the other packages. Sean [[alternative HTML version deleted]]

Hi Junjie. As far as I know, 'affylmGUI' only works on the Affy chips that the 'affy' package works on (e.g. older ones like U133, 4302, etc.) You do have a few options for Exon 1.0 ST in Bioconductor and beyond. Perhaps a good starting point is the 'workflow' page on the BioC site: http://www.bioconductor.org/docs/workflows/oligoarrays/ A non-BioC alternative that has lots of support for Affy arrays in general and Affy Exon 1.0 in particular is aroma.affymetrix: http://groups.google.com/group/aroma-affymetrix/ http://groups.google.com/group/aroma-affymetrix/web/human-exon-array- analysis Hope that helps. Cheers, Mark On 09/04/2009, at 8:14 AM, Junjie Guo wrote: > Hi, I'm a grad student at Johns Hopkins Univ. We are trying to > analyze our > affymetrix Exon Array 1.0 data using affylmGUI. But it seems > bioconductor > does not have the CDF file for this array. Do you have any advice > for me? > > Information of this microarray: > > http://www.affymetrix.com/products_services/arrays/specific/mouse_ex on.affx#1_4 > > > Thanks a lot! > -Junjie > > > -- > ____________________________________________ > Junjie U. Guo, Graduate Student > The Solomon H. Snyder Department of Neuroscience > The Johns Hopkins University School of Medicine > > 733 N. Broadway, BRB 706 > Institute for Cell Engineering - NeuroICE > Hongjun Song Laboratory > Baltimore, MD 21205 > > guojj at jhmi.edu > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852

Did you look at package OneChannelGUI? Narendra >>> Junjie Guo <guojj at="" jhmi.edu=""> 08/04/2009 23:14 >>> Hi, I'm a grad student at Johns Hopkins Univ. We are trying to analyze our affymetrix Exon Array 1.0 data using affylmGUI. But it seems bioconductor does not have the CDF file for this array. Do you have any advice for me? Information of this microarray: http://www.affymetrix.com/products_services/arrays/specific/mouse_exon .affx#1_4 Thanks a lot! -Junjie -- ____________________________________________ Junjie U. Guo, Graduate Student The Solomon H. Snyder Department of Neuroscience The Johns Hopkins University School of Medicine 733 N. Broadway, BRB 706 Institute for Cell Engineering - NeuroICE Hongjun Song Laboratory Baltimore, MD 21205 guojj at jhmi.edu [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Junjie, I am the maintainer of oneChannelGUI. oneChannleGUI is a graphical interface extension of affylmGUI functionalities. It allows the analysis at gene and exon level of exon arrays. A detailed description of the installation procedure is shown in: http://www.bioinformatica.unito.it/oneChannelGUI/ as well in the installation package vignette For any further information and help, feel free to contact me. Cheers Raffaele > ------------------------------ > > Message: 2 > Date: Thu, 09 Apr 2009 12:34:32 +0100 > From: "Narendra Kaushik" <kaushiknk at="" cardiff.ac.uk=""> > Subject: Re: [BioC] Exon Array analysis > To: "Junjie Guo" <guojj at="" jhmi.edu="">, <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <49DDEB580200006C0002DCB1 at zgrw02.cf.ac.uk> > Content-Type: text/plain; charset=US-ASCII > > Did you look at package OneChannelGUI? > > Narendra > > >>>> Junjie Guo <guojj at="" jhmi.edu=""> 08/04/2009 23:14 >>> >>>> > Hi, I'm a grad student at Johns Hopkins Univ. We are trying to analyze our > affymetrix Exon Array 1.0 data using affylmGUI. But it seems bioconductor > does not have the CDF file for this array. Do you have any advice for me? > > Information of this microarray: > > http://www.affymetrix.com/products_services/arrays/specific/mouse_ex on.affx#1_4 > > > Thanks a lot! > -Junjie > > > -- ---------------------------------------- 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