search for: irizary

Hi, i was looking into the documentation for the rma() function in affy() package, and was trying to figure out how exactly the background normalization is done. I read all three papers cited in the rma() documentation, but the most detailed explanation i could find was in Irizary et al., 2003, where they state that they compute B(PM_{ijn}) = E[s_{ijn} | PM_{ijn}] where s_{ijn} is assumed to be exponential, and bg_{ijn} is normal. I still don't understand what value is being computed here, neither am i clear on what the correction looks like. i.e. if s_{ijn} is an...