GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
0
0
Entering edit mode
svlachavas ▴ 780
@svlachavas-7225
Last seen 2 days ago
Germany/Heidelberg/German Cancer Resear…

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 ?

 

affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis • 2.7k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

also your link above doesnt work

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 358 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6