package ‘hugene10stv1.r3cdf’ or ‘hugene10stv1’ is not available
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suparna mitra ▴ 290
@suparna-mitra-5328
Last seen 9.6 years ago
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]]
Annotation Annotation • 2.0k views
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Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
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/hugene1 0stv1cdf.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 at 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 at 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]]
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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]]
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