[BioC] beadarray example data problem

[Mark Dunning]

Hi Keith,

Thanks for letting me know about the problem.

I've looked into it and all that was required was to add an  
"as.character" at the appropriate point when I name the rows in  
assayData. I made the changes and submitted an updated version to  
both release and development version of the package.

Regards,

Mark


On 20 Oct 2006, at 03:06, Keith Satterley wrote:

> Hi Mark or anyone else who can help with the beadarray package,
>
> I'm having trouble getting the beadarray example data to work as  
> described:
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia. 
> 1252;LC_MONETARY=English_Australia. 
> 1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices"  
> "utils"
> "datasets"  "base"
>
> other attached packages:
> beadarray      affy    affyio   Biobase     limma
>    "1.2.1"  "1.12.0"   "1.2.0"  "1.12.0"   "2.9.1"
>
>
> When I load the BSData item and look at BSData, I have the following:
> =====================
>> data(BSData)
>> BSData
> ExpressionSetIllumina (storageMode: list)
> assayData: 47293 features, 18 samples
>    element names: exprs, BeadStDev, NoBeads, Detection
> phenoData
>    rowNames: I.1, IC.1, ..., P42.2 (18 total)
>    varLabels and varMetadata:
>      Sample_Name: Sample_Name
>      Sample_Well: Sample_Well
>      ...: ...
>      Sentrix_Position: Sentrix_Position
>      (7 total)
> featureData
>    featureNames: GI_10047089-S, GI_10047091-S, ..., trpF (47293 total)
>    varLabels and varMetadata: none
> experimentData: use 'experimentData(object)'
> Annotation [1] "Illumina"
> QC Information
>   Available Slots:  Signal StDev Detection
>    featureNames: 1475542110_F, 1475542113_E, 1475542114_A, ...,  
> 1475542113_D,
> 1475542113_F
>    sampleNames: Biotin, cy3_high, cy3_low, ..., pm, negative
> =====================
> When I extract the data files from Rdata.zip in the package's data  
> directory and
> run the following commands from the Example.R file, I have the  
> following:
> =====================
>> targets = readBeadSummaryTargets("targets.txt")
>> targets
>        DataFile               SampleSheet              QCInfo
> 1 raw_data.csv raw_data_sample_sheet.csv raw_data_qcinfo.csv
>> BSData <- readBeadSummaryData(targets)
> Reading file  raw_data.csv
> Reading file  raw_data.csv
>> BSData
> ExpressionSetIllumina (storageMode: list)
> assayData: 47293 features, 18 samples
>    element names: exprs, BeadStDev, NoBeads, Detection
> phenoData
>    rowNames: IH.1, IC.1, ..., P42.2 (18 total)
>    varLabels and varMetadata:
>      Sample_Name: Sample_Name
>      Sample_Well: Sample_Well
>      ...: ...
>      Sentrix_Position: Sentrix_Position
>      (7 total)
> featureData
>    featureNames: 1, 2, ..., 47293 (47293 total)
>    varLabels and varMetadata: none
> experimentData: use 'experimentData(object)'
> Annotation character(0)
> QC Information
>   Available Slots:
>    featureNames: 1475542110_F, 1475542113_E, 1475542114_A, ...,  
> 1475542113_D,
> 1475542113_F
>    sampleNames: Biotin, cy3_high, cy3_low, ..., pm, negative
> =====================
>
> My problem is that I don't have the Target ID's in this second  
> approach. In
> particular note that featureNames in the second approach are not  
> set to the
> TargetIDs as they are in the BSData item.
>
> Can you help me solve this problem,
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
>
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