Thanks Guido, It was really hard to find the exact library. All my tries failed. Thanks, Suaprna. On 18 June 2012 10:46, Hooiveld, Guido <guido.hooiveld@wur.nl> wrote: > Hi, > First of all, please be aware that for the Gene ST arrays 'unofficial' > CDFs are provided. That is, although Affymetrix released a CDF file for > these arrays, these should be considered experimental. > The preferred way of analysing these arrays is through the library 'oligo' > or 'XPS'. They make use of all files provided by Affymetrix (pgf, clf, > annotation CSV, etc). Please see the respective vignettes for more details. > > Having said this, for the analysis you are currently performing you need: > > http://www.bioconductor.org/packages/2.10/data/annotation/html/hugen e10stv1cdf.html > > HTH, > Guido > > --------------------------------------------------------- > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld@wur.nl > internet: http://nutrigene.4t.com > http://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 > > > -----Original Message----- > From: bioconductor-bounces@r-project.org [mailto: > bioconductor-bounces@r-project.org] On Behalf Of suparna mitra > Sent: Monday, June 18, 2012 11:14 > To: bioconductor@r-project.org > Subject: [BioC] package ‘hugene10stv1.r3cdf’ or ‘hugene10stv1’ is not > available > > Hi members, > I'm trying for quite some time to get an analysis started for affy > microarray files which has HuGene-1_0-st-v1. > justrma step worked. > > eset_justrma > ExpressionSet (storageMode: lockedEnvironment) > assayData: 32321 features, 18 samples > element names: exprs, se.exprs > protocolData > sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ... > MC9_(HuGene-1_0-st-v1).CEL (18 total) > varLabels: ScanDate > varMetadata: labelDescription > phenoData > sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ... > MC9_(HuGene-1_0-st-v1).CEL (18 total) > varLabels: sample > varMetadata: labelDescription > featureData: none > experimentData: use 'experimentData(object)' > Annotation: hugene10stv1 > > But I am not able to do the annotation. I tried many possible options. > I keep getting this Error. > > biocLite("hugene10stv1.r3cdf") > Using R version 2.12.2, biocinstall version 2.7.7. > Installing Bioconductor version 2.7 packages: > [1] "hugene10stv1.r3cdf" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘hugene10stv1.r3cdf’ is not available > > > library("annotate") > > library("hugene10stv1") > Error in library("hugene10stv1") : > there is no package called 'hugene10stv1' > > > library("hugene10stv1.db") > Error in library("hugene10stv1.db") : > there is no package called 'hugene10stv1.db' > > > biocLite("hugene10stv1.r3cdf", type = "source") > Using R version 2.12.2, biocinstall version 2.7.7. > Installing Bioconductor version 2.7 packages: > [1] "hugene10stv1.r3cdf" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘hugene10stv1.r3cdf’ is not available > > Can anybody please help. Thanks a lot in advance. > Best wishes, > Suparna. > > [[alternative HTML version deleted]] > > > > -- Dr. Suparna Mitra Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Block A: Waterhouse Buildings, L69 3GL Liverpool Tel. +44 (0)151 795 5414, Internal ext: 55414 M: +44 (0) 7523228621 Email id: smitra@liverpool.ac.uk Alternative Email id: suparna.mitra.sm@gmail.com [[alternative HTML version deleted]]