[BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?

[Stephen Turner]

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 at 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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