[aroma.affymetrix] transcript and exon level analysis for detection of alternative splicings

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[aroma.affymetrix] 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




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[aroma.affymetrix] Re: transcript and exon level analysis for detection of alternative splicings

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:


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/',<a href="http://full.name" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Ffull.name\46sa\75D\46sntz\0751\46usg\75AFQjCNGIfE_b5dc53K_wUBq6Q1AW6d-8Eg';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Ffull.name\46sa\75D\46sntz\0751\46usg\75AFQjCNGIfE_b5dc53K_wUBq6Q1AW6d-8Eg';return true;">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.
 
 
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[aroma.affymetrix] Re: transcript and exon level analysis for detection of alternative splicings

Sanjeev Sariya
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/',<a href="http://full.name" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Ffull.name\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGIfE_b5dc53K_wUBq6Q1AW6d-8Eg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Ffull.name\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGIfE_b5dc53K_wUBq6Q1AW6d-8Eg&#39;;return true;">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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

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