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Question: GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
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gravatar for svlachavas
2.7 years ago by
svlachavas570
Greece/Athens/National Hellenic Research Foundation
svlachavas570 wrote:

Dear ALL,

i have recently acquired some affymetrix CEL files, with genechip Human Transcriptome Array 2.0 in order to identify possible alternative splicing events. As I'm fresh in R and Bioconductor, any tutorials or papers i have found focused on human exon ST 1.0. Thus, i would like to ask if anyone has used the above genechip in R and how much the workflows from human exon ST are different and from some proposed pipelines:

http://www.biomedcentral.com/content/pdf/1471-2164-15-879.pdf

http://www.ncbi.nlm.nih.gov/pubmed/23603090

So  far, i tried to import the CEL files with oligo :

but it doesnt make any sence in summarizing in the probeset level or transcript level

Any suggestions or ideas ?

 

The SCAN algorithm supports this (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). I'd be interested to know your impression on how the results look when you do the summarization at the probeset/transcript levels.

ADD REPLYlink modified 2.7 years ago by Martin Morgan ♦♦ 20k • written 2.7 years ago by Stephen Piccolo500

Thank you Stephen for the above package--i would definately check it, but my main issue as i see from other threads or literature is that there isnt a tutorial or pipeline for HTA-2.0 for exon analysis, such as Human Exon ST-1.0(of course there are quite different genechips). Nevertheless, my other solution would be the open-source application AltAnalyze, for which i found quite interesting(although it is more of an application)

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by svlachavas570

also your link above doesnt work

ADD REPLYlink written 2.7 years ago by svlachavas570
1

The original link included a trailing ')', which I have fixed.

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 20k
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