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