[BioC] MOving from Affy to Lumi: Annotations Problem

[Martin Morgan]

On 12/02/2011 01:38 PM, Thomas H. Hampton wrote:
> My final report text file reads in fine.  Then things get ugly. Any suggestions,
> casual or otherwise, appreciated!
>
> Tom
>
> data<- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")
>
>
>> data
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 47231 features, 12 samples
>    element names: detection, exprs
> protocolData: none
> phenoData
>    sampleNames: 6303230026_A 6303230026_B ... 6303230026_L (12 total)
>    varLabels: sampleID
>    varMetadata: labelDescription
> featureData
>    featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ...
>      N8t5EuJCr0Tk9.zHno (47231 total)
>    fvarLabels: ProbeID TargetID ... DEFINITION (9 total)
>    fvarMetadata: labelDescription
> experimentData: use 'experimentData(object)'
> Annotation: lumiHumanAll.db
>
>
> Data normalization seems not to work. Maybe the final report text files is already normalized..
>
> Next, I want to know what these nuids are, but that goes very poorly.
>
>   getSYMBOL(rownames(exprs(data)), lumiHumanAll.db)
> Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA)
>    error in evaluating the argument 'envir' in selecting a method for function 'mget'

Hi Tim -- I think you're just wanting to supply the annotation db as a 
character string rather than symbol

   getSYMBOL(featureNames(data), annotation(data))

Martin

>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] limma_3.6.9              lumiHumanAll.db_1.12.0   org.Hs.eg.db_2.4.6
>   [4] annotate_1.28.0          lumiHumanIDMapping_1.8.0 RSQLite_0.9-4
>   [7] DBI_0.2-5                AnnotationDbi_1.12.0     lumi_2.2.1
> [10] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
>   [1] affy_1.28.0           affyio_1.18.0         grid_2.12.0
>   [4] hdrcde_2.15           KernSmooth_2.23-6     lattice_0.19-33
>   [7] MASS_7.3-11           Matrix_0.999375-50    methylumi_1.6.1
> [10] mgcv_1.7-6            nlme_3.1-98           preprocessCore_1.12.0
> [13] tools_2.12.0          xtable_1.5-6
>
>
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793