On Mon, Dec 5, 2011 at 8:48 AM, Thomas H. Hampton <
Thomas.H.Hampton@dartmouth.edu> wrote:

> My attempt to create a lumi batch fails when I use a final report text
> file as input.
>
> The text file has the following columns:
>
> [1] "TargetID"                     "ProbeID"
> [3] "X6303230026_A.AVG_Signal"     "X6303230026_A.Detection.Pval"
> [5] "X6303230026_B.AVG_Signal"     "X6303230026_B.Detection.Pval"
> [7] "X6303230026_C.AVG_Signal"     "X6303230026_C.Detection.Pval"
> [9] "X6303230026_D.AVG_Signal"     "X6303230026_D.Detection.Pval"
> [11] "X6303230026_E.AVG_Signal"     "X6303230026_E.Detection.Pval"
> [13] "X6303230026_F.AVG_Signal"     "X6303230026_F.Detection.Pval"
> [15] "X6303230026_G.AVG_Signal"     "X6303230026_G.Detection.Pval"
> [17] "X6303230026_H.AVG_Signal"     "X6303230026_H.Detection.Pval"
> [19] "X6303230026_I.AVG_Signal"     "X6303230026_I.Detection.Pval"
> [21] "X6303230026_J.AVG_Signal"     "X6303230026_J.Detection.Pval"
> [23] "X6303230026_K.AVG_Signal"     "X6303230026_K.Detection.Pval"
> [25] "X6303230026_L.AVG_Signal"     "X6303230026_L.Detection.Pval"
> [27] "SEARCH_KEY"                   "ACCESSION"
> [29] "SYMBOL"                       "PROBE_ID"
> [31] "PROBE_START"                  "CHROMOSOME"
> [33] "PROBE_CHR_ORIENTATION"        "PROBE_COORDINATES"
> [35] "DEFINITION"
>
> I am using the following command to read the data in:
>
> data <- lumiR("FinalReport.txt", lib = "lumiHumanIDMapping")
>
> which finished without error.
>
> > 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
>
> As I understand it, "data" above should be a lumi batch.
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
>
Hi, Tom.

I think you might need to update your R and bioconductor.  I don't know
what the behavior for lumiR was a couple of versions of R ago, but I
believe the current version returns a lumiBatch.

Sean



> 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
>
> Best,
>
> Tom
>
>
>
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>
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