[BioC] package ‘hugene10stv1.r3cdf’ or ‘hugene10stv1’ is not available

[Hooiveld, Guido]

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 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 at r-project.org [mailto:bioconductor-bounces at 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.

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