Hello everybody, first of all, thanks for providing this forum, it really helps me alot in my data analysis. :)
second, my problem: I have 2 costum exon CDFs with CEL files respectively. I want to find differential splicing using FIRMA. It seems that I have after applying the commands from the aroma.org vignette: plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) fit(plmTr, unit=NULL, verbose=verbose, force=force) # this takes a while! firma <- FirmaModel(plmTr) #print(str(firma)) fit(firma, verbose=verbose) # this takes a while! # get the firma scores fs <- getFirmaScores(firma) #print(str(fs)) # take the log2 of the firma scores fsScores <- log2(extractDataFrame(fs)) no group information is available, I have only annotations based on exons: > str(fsScores) 'data.frame': 143259 obs. of 9 variables: $ unit : num 0 1 1.58 2 2.32 ... $ group : num 0 0 0 0 0 0 0 0 0 0 ... $ cell : num 0 1 1.58 2 2.32 ... $ caquinof_20090625_Flower1_Affy_new-v4: num 0.235 -0.183 -0.177 -0.111 -0.094 ... $ caquinof_20090625_Flower2_Affy_new-v4: num 0.02462 -0.21418 -0.00289 -0.04531 0.03572 ... $ caquinof_20090625_Flower3_Affy_new-v4: num -0.0528 -0.2674 0.0483 -0.0398 -0.0789 ... $ caquinof_20090625_Leaf1_Affy_new-v4 : num -0.0151 -0.1455 -0.3472 -0.2368 -0.0481 ... $ caquinof_20090625_Leaf2_Affy_new-v4 : num -0.207 -0.0648 -0.1754 -0.1012 -0.4942 ... $ caquinof_20090625_Leaf3_Affy_new-v4 : num -0.194 0.1359 0.1802 -0.4697 0.0343 ... were variables 4-6 are flower replicates and 7-9 leaf replicates of arabidopsis plant. But I can get the group information (exons per transcript) from the exon annotation: one example: exon annotation = 'AT1G01040.0.Chr1.plus.26862.27012' transcript annotation = 'AT1G01040.0' Now, I want to 'insert' the transcript annotation as 'group' variable and I found the method 'SetMergeGroup': I tried to use it like this: setMergeGroups(groupSet[,2]) but then comes the Error Fehler in UseMethod("setMergeGroups") : nicht anwendbare Methode für 'setMergeGroups' auf Objekt der Klasse "c('double', 'numeric')" angewendet which means this: Error in UseMethod("setMergeGroups"): not applicable method for 'setMergeGroups' for object of the class "c('double', 'numeric')" applied. Could you tell me how to use tis method properly? Do I have some wrong assumptions in my data processing step? thanks alot for your expertise in advance, Best wishes, Marlen Müller Masterstudent at the Plant Biotechnology Group, ETH Zurich -- 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 aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/