[BioC] vsn + backgroundSubtract

Wolfgang Huber huber at ebi.ac.uk
Thu Jul 3 23:19:47 CEST 2008

Dear David,

please provide the output of sessionInfo() and a reproducible example, 
otherwise it is difficult to give a concrete reply.

Also, please use the function "vsn2" instead of "vsn" (both in the 
package vsn).

 From your message it appears (sorry if my guess is wrong - see above) 
as if you use an RGList for one color data - which, if true, would be 
weird. Have you tried putting the data into an ExpressionSet and then 
calling vsn2/justvsn on that?

  Best wishes

Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

> Hi Wolfgang and list,
> Is it possible to do vsn() or justvsn() with backgroundSubtract=TRUE for 
> a one-color genepix chip? I tried and received an error saying that 
> "object R was not found". Could I fool the function duplicating G and Gb 
> into R and Rb or will the normalisation result then be modified and get 
> erroneous output??
> Thanks for your help,
> David
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