transcript and exon level analysis for detection of alternative splicings

[jjspring OH]

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

[jjspring OH]

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:

[Sanjeev Sariya]

Hi Sunghee,

Did you figure this out? I'm in the same boat.