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="" annotation="" html="" mi="" rna10cdf.html=""> mirna10cdf and <http: www.bioconductor.org="" help="" bioc-="" views="" release="" data="" annotation="" 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 [[alternative HTML version deleted]]

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 D?ring > 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 D?ring > > > > > > > [[alternative HTML version deleted]] > >