I would like to compare the results from plmTr and plmEx, estimation of overall expression for transcripts and exon-by-exon estimation, but when i tried to run ExonRmaPlm with mergeGroups = T and F, respectively, i am getting the identical results for following objects including FIRMA scores based on 29170 rows by samples, plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) print(plmEx) ... firma <- FirmaModel(plmEx) fit(firma, verbose=verbose) fs <- getFirmaScores(firma) asData <- extractDataFrame(fs, addNames=TRUE) > fs <- getFirmaScores(firma) > asData <- extractDataFrame(fs, addNames=TRUE) > dim(asData)  29170 13 Yet, And also, when i ran previously in oligo library, got 213067 probe indices library(oligo) celFiles = list.celfiles( '/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T) raw = read.celfiles(celFiles) exon_rma = rma(raw,target="probeset") #pre-processing/normalization/log2-scale exon_mat <- exprs(exon_rma) dim(exon_mat) head(exon_mat) > dim(exon_mat)  213067 8 My questions, first question is how i can get different sets from transcript and exon-by-exon from cell files? and also, just curious, how is it mapped from probe sets (213K) onto transcript/exon level annotation(29K)? And, major interest is to detect differentially alternative splicings for each gene? (we are mostly interested in looking at those genes, e.g. Although a gene is differentially expressed but it is not differentially expressed in AS or vice versa,) how can i extract these information from FIRMA scores? could you pls let me know ? Thanks a lot in advance, Sunghee -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to email@example.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.