[BioC] lumi: how is the controlData to be read and used?
Gordon Smyth
smyth at wehi.EDU.AU
Sat Oct 27 07:12:04 CEST 2007
The lumi package functions lumiB() and bgAdjust() mention the fact
that control data can be used to background correct Illumina data.
There is however no documentation regarding what the control data
should contain, how it should be read it in, or exactly how it is used.
I have summary probe profile data output from BeadStudio (not
normalized or background corrected):
Sample_Probe_Profile.txt
I also have summary control probe data. This includes both positive
and negative control probes:
Control_Probe_Profile.txt
How is it recommended that I read and use the control data, prior to
using lumiT(method="vst")? A complete code example would be helpful.
Gordon
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