Hi Max. Short answer is yes, you should log2 the stored FIRMA values. And, same for the ChipEffectSet from your plmTr object.
It's just that the CEL file format doesn't store negative numbers so even though things are calculated on log2 intensities (i.e. model fit, FIRMA calculations, etc) everything is *stored* on the 2^X scale when saved to disk. For example, if you look at the code examples in the following thread for pulling out the FIRMA scores, log2 is applied before the limma analysis: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/36d8c59d742fc503/ Hope that helps. Mark > > Hi, > I have a pretty basic question: > > I replicated the vignette from the website to analyze my six HuEx-1_0- > st-v2 arrays (falling in 2 groups) and everthing worked fine. > > The firma scores I get range between 0 and ~6000, but histogram peaks > around 1. So before doing limma on the firma scores one should log > them (I assume the values in Fig2 of the paper are also logged). > > Therefore I wondered whether it would be appropriate to log already > the plmTr values? > > Thanks! > max > > > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
