Hi, all: I am trying to understand the supplementary text of the original FIRMA paper published in Bioinformatics last year. the S1 figure shows UNR gene about its exon effect removed or retained. I am confused about the plots. what are the y-axis? Are they residuals from RMA fit , after running ExonRMAPlm?
Let d be the normalized intensity (log2), r as the residual from plm fit (log2), p as the probe affinity. I would assume S1(a) is just simple plot of d-p, S1(b) as d-p+estimated e(j)? Am I correct? If that is the case, S1(a) should show exact same information as plot of d because for all arrays, the probe affinity should be the same? But from the figures, how can I tell where the splicing events occur? I am puzzled because I thought it should also remove gene effect (chip effect)? Can some one explain it to me? Thanks Sabrina --~--~---------~--~----~------------~-------~--~----~ 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 aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
