[BioC] How to remove probes from Illumina data?

Matt Ritchie Matt.Ritchie at cancer.org.uk
Wed Mar 12 23:26:17 CET 2008

Hi Alice,

You could try setting the 'probes' argument in createBeadSummaryData() - if
you set it to a vector containing IDs for the non-control bead types, you
should end up with summarised data for these beads only.

If this doesn't work for you, or if you tried something else in beadarray
that you thought should work, and it failed, please send us an example of
the code you ran so that we may fix whatever is wrong.

Best wishes, 


> Hello,
> I have bead-level data from an Illumina expression experiment.  I have
> background corrected and summarised the data, but I need to take the
> control probes information out of the ExpressionSetIllumina object, or
> remove them from the beadlevel list.  I have tried a few things but they
> stop me from using the object any further.  Could someone please suggest
> a correct way I could go about this?
> Thank you.
> Alice Johnstone

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