[BioC] Cannot Subset Columns in beadarray package, ExpressionSetIllumina Class in R-2.8.0, BioBase 2.2.1, beadarray 1.10.0

[Julian Lee]

Hi Mark and Others,

I'm having some problems with the new beadarray package. I can't subset the columns,

Example
>library(beadarray)
Loading required package: limma
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: hwriter
Loading required package: sma

Attaching package: 'beadarray'


	The following object(s) are masked from package:limma :

	 backgroundCorrect,
	 imageplot,
	 plotMA 

> data(BSData)
> BSData
ExpressionSetIllumina (storageMode: list)
assayData: 1471 features, 10 samples 
  element names: exprs, se.exprs, NoBeads 
phenoData
  rowNames: 1318758_R007_C004, 1318791_R002_C006, ..., 1318758_R002_C002  (10 total)
  varLabels and varMetadata description:
    arrayName: NA
featureData
  featureNames: 2, 3, ..., 6140  (1471 total)
  fvarLabels and fvarMetadata description:
    ProbeID: NA
experimentData: use 'experimentData(object)'
Annotation: illuminaProbeIDs 
QC Information
 Available Slots:  exprs se.exprs NoBeads controlType
  featureNames: 
  sampleNames: 

> BSData[,1:2]
Error: subscript out of bounds

##Other Examples
> dataFile<-'for_R.txt'
> sampleSheet<-'SampleSheet.csv'
> readBeadSummaryData(dataFile=dataFile,skip=0,ProbeID='TargetID',sampleSheet=sampleSheet)->BSData2
> BSData2
ExpressionSetIllumina (storageMode: list)
assayData: 27578 features, 24 samples 
  element names: exprs, se.exprs, NoBeads, Detection 
phenoData
  rowNames: AGS, AZ521, ..., Methylated  (24 total)
  varLabels and varMetadata description:
    Sample_Name: Sample_Name
    Sample_Well: Sample_Well
    ...: ...
    Unique: Unique
    (8 total)
featureData
  featureNames: cg00000292, cg00002426, ..., cg27665659  (27578 total)
  fvarLabels and fvarMetadata description:
    ProbeID: NA
experimentData: use 'experimentData(object)'
Annotation:  
QC Information
 Available Slots:  exprs se.exprs NoBeads controlType
  featureNames: 
  sampleNames: 
> BSData2[,1:2]
Error: subscript out of bounds


No errors are reported while reading the data into R.  

However, this works on my older Windows R-2.7.1 on Beadarray 1.8.0. 

ps - Katrina Bell, if you're reading this, I'm playing with the new Infinium 27k methylation dataset.

regards
julian






> sessionInfo()
R version 2.8.0 (2008-10-20) 
i486-pc-linux-gnu 

locale:
LC_CTYPE=en_SG.UTF-8;LC_NUMERIC=C;LC_TIME=en_SG.UTF-8;LC_COLLATE=en_SG.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_SG.UTF-8;LC_PAPER=en_SG.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_SG.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] beadarray_1.10.0    sma_0.5.15          hwriter_0.93       
 [4] geneplotter_1.20.0  annotate_1.20.1     xtable_1.5-4       
 [7] AnnotationDbi_1.4.2 lattice_0.17-17     Biobase_2.2.1      
[10] limma_2.16.3       

loaded via a namespace (and not attached):
[1] DBI_0.2-4          grid_2.8.0         KernSmooth_2.22-22 RColorBrewer_1.0-2
[5] RSQLite_0.7-1   



-- 
Julian Lee
Bioinformatics Specialist
Cellular and Molecular Research
National Cancer Center Singapore