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/hugene10stv1cdf.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.
>
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>
>
>
>


-- 
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

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