[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



More information about the Bioconductor mailing list