the question i would like to ask is more general for the context of the group, but highly related to an R package, that's why i finally created this post. In detail, because i'm making a study-presentation for university needs regarding normalization methodologies/algorithms in high-throughput methodologies, i would like to ask something specific but very important about the background correction implemented with GCRMA algorithm. Specifically, i would like to ask in the R package gcrma(the latest versions at least), as in the argument "type" the default is the "full model" : that means that firstly the MM probe intensities are firstly "adjusted"-(corrected) based on probe affinity information, and then subtracted from the PM intensities ? And subsequently, the general rationale of this adjustment is that is has been described that MM intensities often measure signal except from background noise and more often yield higher intensity levels than PM intensity probes ??
Thank you in advance,