Hi Raj,

You should be able to achieve what you want by using the useSampleFac
argument to the summarise function

summaryData <- summarize(beadLevelData, useSampleFac=T, sampleFac =
rep(LETTERS[1:12], each=2)

The resulting summary object should now have 12 arrays rather than 24

Hope this helps,

Mark


On Fri, Apr 26, 2013 at 3:45 AM, RS [guest] <guest@bioconductor.org> wrote:

>
> Hi Mark and Matt,
>
> I have four samples with three replicates for which Illumina beadarray
> expression data was collected. The array design corresponds to the
> HumanHT12 chip with Humanv4 annotation.
>
> I started with beadlevel data with .tif files, .locs files and
> _perBeadFile.txt and was able to use processSwathData() function to obtain
> 24 _Swath.tif files. My sampleSheet.csv had issues although I prepared it
> based on the beadlevel example data you provide. So, I didn't provide this
> file and used readIllumina() to read the 24 _Swath.tif files. It read the
> files fine but it's not clear how to combine the two files into one
> intensity file per array/sample? I would like to create an expressionSet
> and perform differential expression using limma.
>
> I would appreciate any help.
>
> Thanks,
> Raj
>
>
>  -- output of sessionInfo():
>
> None
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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