[BioC] Using gcrma with \"Affymetrix GeneChip miRNA v1.0\" data

[Sean Davis]

Hi, Scott.

See below.

On Sat, Jul 13, 2013 at 2:03 PM, Scott Robinson [guest]
<guest at bioconductor.org> wrote:
>
> Dear List,
>
> I am working with some "Affymetrix GeneChip miRNA v1.0" chip data and am recieving an error upon executing the gcrma method. Is this error to do with the NSB estimation by any chance? If so is my only solution to use simply rma instead?
>
> Thanks,
>
> Scott
>
>
>> celFiles <- read.affy()
>> celFiles
> trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/mirna102xgaincdf_2.12.0.zip'
> Content type 'application/zip' length 225057 bytes (219 Kb)
> opened URL
> downloaded 219 Kb
>
> The downloaded binary packages are in
>         C:\Users\Scott\AppData\Local\Temp\RtmpQxcEYA\downloaded_packages
> Loading required package: AnnotationDbi
>
> AffyBatch object
> size of arrays=230x230 features (66 kb)
> cdf=miRNA-1_0_2Xgain (7815 affyids)
> number of samples=175
> number of genes=7815
> annotation=mirna102xgain
> notes=
> Warning message:
> package ‘AnnotationDbi’ was built under R version 3.0.1
>> celFiles.gcrma <- gcrma(celFiles)
> Adjusting for optical effect...............................................................................................................................................................................Done.
> Computing affinities[1] "Checking to see if your internet connection works..."
> [1] "Environment mirna102xgainprobe was not found in the Bioconductor repository."
> Error in get(probepackagename) : object 'mirna102xgainprobe' not found

gcrma needs to have the actual probe sequences.  These are contained
in a "probe" package and there is no such package available.
I have not kept up with how to make such a probe package from scratch,
so I won't comment directly.  Hopefully, someone else will chime in
here.

Yes, rma should not need the probe package, so that should probably
work for you.

Sean


>  -- output of sessionInfo():
>
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] mirna102xgaincdf_2.12.0 AnnotationDbi_1.22.6    affyPLM_1.36.0
>  [4] preprocessCore_1.22.0   simpleaffy_2.36.1       gcrma_2.32.0
>  [7] genefilter_1.42.0       affy_1.38.1             Biobase_2.20.0
> [10] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.28.0        annotate_1.38.0      BiocInstaller_1.10.2
>  [4] Biostrings_2.28.0    DBI_0.2-7            IRanges_1.18.1
>  [7] RSQLite_0.11.4       splines_3.0.0        stats4_3.0.0
> [10] survival_2.37-4      tools_3.0.0          XML_3.98-1.1
> [13] xtable_1.7-1         zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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