Dear Olivia, if you wish to analyze gene arrays using a graphical interface you can also use oneChannelGUI (http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html), which extends the functionalities of affylmGUI and uses apt tools, from Affymetrix, to intensity calculations, so you do not need cdf. Affy libraries and gene data annotation are derived from Affymetrix and embedded internally. Feel free to contact me if you need extra info on oneChannelGUI installation and usage. Cheers Raffaele Date: Tue, 22 Sep 2009 14:21:42 +0200 From: Prazeres da Costa Olivia <olivia.dacosta@mikrobio.med.tum.de> Subject: [BioC] Bioconductor does not provide Humane gene ST annotation "hugene10stv1cdf" to work with affylmGUI?! To: "'bioconductor at stat.math.ethz.ch'" <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <80E715FF2567EF4C97E1B96F4B16FC4A0D2189D4EC at mail.drvis.de> Content-Type: text/plain Dear all, I would like to use the affylmGUI package to analyze some Affymetrix Human Gene ST arrays. But it seems that Bioconductor does not provide the annotation package hugene10stv1cdf yet - which is needed to work with the affylmGUI library. I get the following error message: Error in getCdfInfo(object): Could not obtain CDF environment, problems encountered: Specified environment does not contain GuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available. How can I proceed to work with the affylmGUI package? Is there a "hugene10stv1cdf" annotation package available, and where do I have to install it, so that I can work with the affylmGUI library? Thanks for any help! Olivia -- ---------------------------------------- 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