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

Stephen Turner vustephen at gmail.com
Thu Nov 8 23:25:12 CET 2012


Thanks much. I used read.celfiles() and rma() worked perfectly at this
point. I will definitely take you up on help getting this to gel with
the rest of my workflow.

My next step with gene ST arrays is to annotate the expressionset
object with fData, such that when I use topTable() later on, all my
results are annotated. E.g.:

## Which annotation package are you using?
eset at annotation
annodb <- "hugene10sttranscriptcluster.db"

## Annotate the features
ls(paste("package:", annodb, sep=""))
ID     <- featureNames(eset)
Symbol <- as.character(lookUp(ID, annodb, "SYMBOL"))
Name   <- as.character(lookUp(ID, annodb, "GENENAME"))
Entrez <- as.character(lookUp(ID, annodb, "ENTREZID"))
tmp <- data.frame(ID=ID, Entrez=Entrez, Symbol=Symbol, Name=Name,
stringsAsFactors=F)
tmp[tmp=="NA"] <- NA
fData(eset) <- tmp

But I'm not sure what to do here because ls("package:pd.mirna.3.0")
doesn't return what the typical hu/mogene10sttranscriptcluster.db DBs
return.

Many thanks,

Stephen

On Thu, Nov 8, 2012 at 10:32 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> 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 at 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 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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