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)


plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)



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 


celFiles = list.celfiles(
'/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T)

raw = read.celfiles(celFiles)

exon_rma = rma(raw,target="probeset")  

exon_mat <- exprs(exon_rma)



> 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, 


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.

Reply via email to