[BioC] miRNA Array from Affymetrix

[Hooiveld, Guido]

Hi Claudia,
I have used the same arrays as well, and did not expercience any problem. Based on the error it indeed has something to do with the CDF environment that is not properly recognized. It should be 'miRNA-1_0' without the _2Xgain attached to it... Why this in your case is added is difficult to find out without your code and sessionInfo.

As you can see below his works for me using 6 sample miRNA files.

HTH,
Guido



> library(affy)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

>
> affy.data <- ReadAffy()
> affy.data
AffyBatch object
size of arrays=230x230 features (12 kb)
cdf=miRNA-1_0 (7815 affyids)
number of samples=6
number of genes=7815
annotation=mirna10
notes=
> x.norm <- rma(affy.data)
Background correcting
Normalizing
Calculating Expression
> x.norm
ExpressionSet (storageMode: lockedEnvironment)
assayData: 7815 features, 6 samples 
  element names: exprs 
protocolData
  sampleNames: Z001_101_LF_LIVER_(MIRNA-1_0).CEL
    Z001_102_LF_LIVER_(MIRNA-1_0).CEL ...
    Z001_118_LF_LIVER_(MIRNA-1_0).CEL (6 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: Z001_101_LF_LIVER_(MIRNA-1_0).CEL
    Z001_102_LF_LIVER_(MIRNA-1_0).CEL ...
    Z001_118_LF_LIVER_(MIRNA-1_0).CEL (6 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mirna10 
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mirna10cdf_2.7.0 affy_1.28.0      Biobase_2.10.0  

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.0         
> 

------------------------------------------------ 
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 
internet:   http://nutrigene.4t.com
email:      guido.hooiveld at wur.nl



> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of 
> Claudia Döring
> Sent: Monday, December 06, 2010 16:10
> To: bioconductor at r-project.org
> Subject: [BioC] miRNA Array from Affymetrix
> 
> Dear Sir and Madam, 
> 
> 
> 
> I have a problem with the miRNA Microarray from Affymetrix.
> 
>  
> 
> I get the follow error message:
> 
>  
> 
> AffyBatch object
> 
> size of arrays=230x230 features (11 kb)
> 
> cdf=miRNA-1_0_2Xgain (??? affyids)
> 
> number of samples=9
> 
> Error in getCdfInfo(object) : 
> 
>   Could not obtain CDF environment, problems encountered:
> 
> Specified environment does not contain miRNA-1_0_2Xgain
> 
> Library - package mirna102xgaincdf not installed
> 
> Bioconductor - mirna102xgaincdf not available
> 
> In addition: Warning message:
> 
> missing cdf environment! in show(AffyBatch)
> 
>  
> 
> I installed
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/mi
> rna10cdf.html> mirna10cdf and
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/mi
> rna10probe.html> mirna10probe. R und Bioconductor are 
> installed last week, but also in older versions it doesn't work.
> 
>  
> 
> Thank you very much
> 
>  
> 
> Claudia Döring  
> 
>  
> 
>  
> 
> 
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>