Hi, all A quick question about using lmFit on firma scores from exon array analysis. According to the vignettes, to detect splicing events, we need to use lmFit to find the significant event as following (my code so far):
fit <- lmFit(exFirma[,3:ncol(exFirma)] ,design) fit2<-contrasts.fit(fit,cont.matrix); fit2<-eBayes(fit2,proportion=p); topList<-topTable(fit2,coef=contrast[k],adj="fdr"); What this does, to my understanding, is to find firma scores that are significantly different between your contrast groups, say one group is all negative, the other is all positive. But we know exon splicing event is not usually 100%, so it is very likely some samples in one group have -4, -3, and the others in the same group might be 1 or 0.5. but if that is the case, since lmFit basically uses the moderated t- test, will it detect this as significant? If what I just described is reasonable, then will I be better off if I just use the m=median(firma score) for each group and rank the the differences of my contrast group (m1-m2) and find out the most potential splicing events? I guess I am a little bit confused. 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
