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

[James W. MacDonald]

Hi Stephen,

Substitute with

library(oligo)
affybatch <- read.celfiles(list.celfiles())
eset <- rma(affybatch)

Best,

Jim



On 11/8/2012 10:12 AM, Stephen Turner 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 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099