Hi Sunghee, Did you figure this out? I'm in the same boat.
On Sunday, 21 September 2014 22:19:09 UTC-4, Sunghee Oh wrote: > > > > > And one more question: > > On the FIRMA scores, what are NA values, though expression levels are not > zero? > > > Thanks, > > > Sunghee > > > > 2014년 9월 22일 월요일 오전 10시 50분 25초 UTC+9, jjspring OH 님의 말: >> >> >> >> Hi, >> >> >> 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) >> >> [1] 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) >> >> [1] 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 aroma-affymetrix@googlegroups.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.
