Hi Jenny,

Sorry to hear that subsetting isnšt quite working as you would expect.
Using the example data set available with the beadarray package I am able to
subset probes/samples in the usual way without error.  Do the following
commands work ok for you?

Best wishes,

Matt

> library(beadarray)
> data(BSData)
> dim(BSData)
Features  Samples 
   47312       18
> sub1 = BSData[,1:6]
> dim(sub1)
Features  Samples 
   47312        6
> sub2 = BSData[1:6,]
> dim(sub2)
Features  Samples 
       6       18
> sub3 = BSData[11:20,4:7]
> dim(sub3)
Features  Samples 
      10        4
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] beadarray_1.8.0      affy_1.18.0          preprocessCore_1.2.0
affyio_1.8.0       
 [5] geneplotter_1.18.0   annotate_1.18.0      xtable_1.5-2
AnnotationDbi_1.2.0
 [9] RSQLite_0.6-8        DBI_0.2-4            lattice_0.17-6
Biobase_2.0.0      
[13] limma_2.14.0  

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22 RColorBrewer_1.0-2 grid_2.7.0


On 22/5/08 19:36, "Jenny Drnevich" <drnevich@illinois.edu> wrote:

> Hi,
> 
> I have an ExpressionSetIllumina object with 12 samples. Is there a way to
> subset on the samples and create a new ExpressionSetIllumina object? The
> description of the ExpressionSetIllumina class has a combine() method for two
> ExpressionSetIllumina objects, and also has this:
> 
> object[(index): Conducts subsetting of matrices and phenoData and reporterInfo
> components # shouldn't this read object[(index)]: ?
> 
> It appears this subsetting works on the features, not samples:
> 
>> > dim(BS.bg.quant)
> Features  Samples
>    45281       12
> 
>> > temp <- BS.bg.quant[1:6]
>> > dim(temp)
> Features  Samples
>       6       12 
> 
> Trying to subset on samples/columns like you can do for other ExpressionSet
> objects yields this:
> 
>> > temp <- BS.bg.quant[,1:6]
> Error: subscript out of bounds
> 
> 
> Is there a way to subset on samples, or is there a reason why I shouldn't
> subset the object but instead create a new one using readBeadSummaryData?
> 
> Thanks,
> Jenny


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