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
>
>
>
>
>
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