Question: GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
gravatar for svlachavas
3.6 years ago by
Greece/Athens/National Hellenic Research Foundation
svlachavas610 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:

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 ( 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 3.6 years ago by Martin Morgan ♦♦ 22k • written 3.6 years ago by Stephen Piccolo530

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 3.6 years ago • written 3.6 years ago by svlachavas610

also your link above doesnt work

ADD REPLYlink written 3.6 years ago by svlachavas610

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

ADD REPLYlink written 3.6 years ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 369 users visited in the last hour