The problem is that you have both affy and oligo loaded simultaneously
(I'll add this to my todo list, so in the future users do not need to worry
about it).

Option 1)  (don't load oligo)

By using ReadAffy(), you're importing the data via affy package, which does
not know how to handle miRNA-3.0 arrays.

If you rather stick to your original workflow, you'd need to follow the
"unrecommended" path of converting a PGF to a CDF (I rather not say much
about this), and then build the required annotation packages yourself.


Option 2) (don't load affy)  (disclaimer: I'm the author of oligo)

If you don't load affy and use read.celfiles (from oligo), you'll get the
rma() part done easily. At this point, I'd be happy to work with you to
incorporate tools to simplify the use of the other packages that you have
in your workflow.


best,
benilton


On 8 November 2012 15:12, Stephen Turner <vustephen@gmail.com> wrote:

> Just wanted to resurrect this issue. I routinely analyze gene 1.0 ST
> chips in my core, but this is the first time I'm looking at the miRNA
> 3.0 chip (or any Affy miRNA chip for that matter).
>
> I understand that there's no 3.0 CDF environment available. How might
> I go about building one and incorporating that into my workflow?
>
> My typical [Hu/Mo]Gene 1.0 ST workflow goes something like this:
>
> ############################################
> ## Load data
> affybatch <- ReadAffy(filenames)
> eset <- rma(affybatch)
>
> ## Annotate
> ID <- featureNames(eset)
> Symbol <- as.character(lookUp(ID, "hugene10sttranscriptcluster.db",
> "SYMBOL"))
> Name <- as.character(lookUp(ID, "hugene10sttranscriptcluster.db",
> "GENENAME"))
> fData(eset) <- data.frame(ID=ID, Symbol=Symbol, Name=Name)
>
> ## Typical QC with arrayQualityMetrics and analysis with limma
> ############################################
>
> I'm getting this error when using rma() on the affybatch object:
>
> > rma(affybatch)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "rma", for signature
> "AffyBatch"
>
> And additionally when I try to view the affybatch:
>
> AffyBatch object
> size of arrays=541x541 features (19 kb)
> cdf=miRNA-3_0 (??? affyids)
> number of samples=6
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain miRNA-3_0
> Library - package mirna30cdf not installed
> Bioconductor - mirna30cdf not available
>
> Thanks.
>
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
>  [1] pd.mirna.3.0_3.6.0         oligo_1.22.0
> oligoClasses_1.20.0
>  [4] RSQLite_0.11.2             DBI_0.2-5
> biomaRt_2.14.0
>  [7] VennDiagram_1.5.1          SPIA_2.8.0
> pvclust_1.2-2
> [10] genefilter_1.40.0          gplots_2.11.0              MASS_7.3-22
> [13] KernSmooth_2.23-8          caTools_1.13
> bitops_1.0-4.1
> [16] gdata_2.12.0               gtools_2.7.0
> limma_3.14.1
> [19] arrayQualityMetrics_3.14.0 annotate_1.36.0
> AnnotationDbi_1.20.2
> [22] affy_1.36.0                Biobase_2.18.0
> BiocGenerics_0.4.0
> [25] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.30.0     affyio_1.26.0         affyPLM_1.34.0
> beadarray_2.8.1
>  [5] BeadDataPackR_1.10.0  Biostrings_2.26.2     bit_1.1-9
> Cairo_1.5-1
>  [9] cluster_1.14.3        codetools_0.2-8       colorspace_1.2-0
> ff_2.2-9
> [13] foreach_1.4.0         gcrma_2.30.0          GenomicRanges_1.10.3
> Hmisc_3.10-1
> [17] hwriter_1.3           IRanges_1.16.4        iterators_1.0.6
> lattice_0.20-10
> [21] latticeExtra_0.6-24   parallel_2.15.0       plyr_1.7.1
> preprocessCore_1.20.0
> [25] RColorBrewer_1.0-5    RCurl_1.95-1.1        reshape2_1.2.1
> setRNG_2011.11-2
> [29] splines_2.15.0        stats4_2.15.0         stringr_0.6.1
> survival_2.36-14
> [33] SVGAnnotation_0.93-1  tools_2.15.0          vsn_3.26.0
> XML_3.95-0.1
> [37] xtable_1.7-0          zlibbioc_1.4.0
>
>
> On Sat, Oct 13, 2012 at 12:56 AM, Dana Most <danamost@gmail.com> wrote:
> > Hi All,
> >
> > Have you managed to find a cdf for the miRNA 3.0?
> > I keep getting the error : "...cdf=miRNA-3_0 (??? affyids)..."
> >
> > When I spoke to Affymetrix they said that the 3.0 version doesn't have a
> > .cdf and that a .cdf format wouldn't be compatible...
> > They said I should use the 'xps' package on the bioconductor website
> > together with a .pgf from their website.
> > 'xps' doesn't work with Windows 7, which unfortunately is what I have.
> >
> > Can anyone help me?
> >
> > Thanks,
> >
> > Dana
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor@r-project.org
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>
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