Hi Darren,

I'm having a little trouble trying to reproduce the error. What commands
did you use to generate the bead-level data? It seems to work for the data
that I have.

In the meantime, you can force beadarray to consolidate sections by using
the sampleFac argument. The resulting object will then have all columns
(samples).

> bsd <- summarize(bld,useSampleFac=T,sampleFac=rep(1:12,each=2))

> bsd
ExpressionSetIllumina (storageMode: list)
assayData: 48107 features, 12 samples
  element names: exprs, se.exprs, nObservations
protocolData: none
phenoData
  rowNames: 8106854095_A 8106854095_B ... 8106854095_L (12 total)
  varLabels: sampleID SampleFac
  varMetadata: labelDescription
featureData
  featureNames: ILMN_1802380 ILMN_1893287 ... ILMN_1806862 (48107
    total)
  fvarLabels: ArrayAddressID IlluminaID Status
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: Humanv4
QC Information
 Available Slots:
  QC Items: Date, Beadchip, ..., SampleGroup, numBeads
  sampleNames: 8106854095_A-Swath1, 8106854095_A-Swath2, ...,
8106854095_L-Swath1,
8106854095_L-Swath2

Please send me your code though.

Regards,

Mark



On Wed, Jun 5, 2013 at 9:43 AM, Darren <darren.plant@manchester.ac.uk>wrote:

> Sunitha M <sunkorner@...> writes:
>
> >
> > Dear all,
> >
> > I am trying to analyse Illumina beadarray data produced by iScan for the
> first time. This scanner saves each
> > array in two different tiff images. As a first step, I used
> ProcessSwathData() function that
> > deconvolutes the bead-level data and creates two files, swath1 and
> swath2 for the two tiff images.
> > However, in the subsequent step, i. e. readIllumina function these two
> files are treated as if they are
> > from two different arrays (although they belong to one array). Is there
> any parameter we can pass to the
> > readIllumina function to indicate that those two files belongs to one
> array.
> >
> > Any help in this regard is highly appreciated.
> >
> > Thanks
> >
> > Sunitha
> >
> >       [[alternative HTML version deleted]]
> >
> >
> > Dear Sunitha,
> i hope you don't mind me joining in but i am faced with the same problem.
> There is no information on how to proceed with iScan data after
> ProcessSwathData() as far as i can see. Please let me know if you figure
> this out. I think others have used Illumina software to process the tiff
> files as an alternative.
> Best wishes,
> Darren
>
> > _______________________________________________
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