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

[Scott Robinson [guest]]

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

 -- 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      

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