[BioC] Question regarding bg correction/normalization/summarization

[Tova Fuller]

Hello!

I was wondering about the terminology used to describe VSN in its 
vignette.  The vignette claims VSN does calibration, and mentions 
something about comparison against background - so, in addition to 
normalization, does VSN do background correction?  The example given 
for use with the affy package has bg correction turned off, but I've 
notice several posters have used rma for background correction with vsn 
in expresso.

Also, I was curious as to opinions regarding which possible 
combinations in expresso or threestep (affyPLM), in addition to DChip & 
PLIER are most common for doing bg correction, normalization & 
summarization.  Or which combos are the best.  Any feedback would be 
wonderful.

Thank you, and I apologize for these probably trivial questions - I am 
but a lowly graduate student.

Thanks again,

Tova Fuller