SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count da Newsbot! Literature Watch 0 11-18-2011 02:20 AM
RNA-Seq: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Newsbot! Literature Watch 0 10-15-2011 03:11 AM
Where could I get a set of real RNA-Seq data Hunny Bioinformatics 5 04-19-2011 11:57 AM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses. Newsbot! Literature Watch 0 01-22-2011 02:02 AM
RNA-Seq data set? simon8udke RNA Sequencing 1 04-15-2010 12:20 PM

Reply
 
Thread Tools
Old 04-12-2012, 01:26 PM   #1
jel4h
Junior Member
 
Location: USA

Join Date: Apr 2012
Posts: 3
Default Gene set enrichment analysis of RNA-Seq data

I was wondering if anyone is aware of a gene
set enrichment algorithm for RNA-Seq data that:

1) does not require a specification of differentially
expressed (DE) genes (i.e.no need to use a hard
p-value threshold cutoff for determining the DE gene
list)

2) uses subject sampling instead of gene sampling
to obtain the p-value (i.e.this would maintain
gene-gene correlations)

Basically, I'm looking for a
self-contained/subject sampling method (e.g.
SAM-GS for microarray data) or a "hybrid" method
(e.g. GSEA for microarray data). The only gene set
enrichment algorithm that I am aware of for RNA-Seq
data is GOSeq, but it uses a competitive/gene
sampling method (i.e. Fisher's Exact Test).
Note, the ideas of self-contained vs competitive and
subject sampling vs gene sampling come from the
following paper: Goeman JJ, Bühlmann P.Analyzing
gene expression data in terms of gene sets:
methodological issues. Bioinformatics. 2007 Apr 15;23(8)

Something like GSEA-SNP is close to what I want.
It uses a test-statistic that is suitable for discrete data
and uses subject sampling to calculate the p-values.

Thanks,
Julie
jel4h is offline   Reply With Quote
Old 06-21-2012, 04:25 AM   #2
ninni
Junior Member
 
Location: london

Join Date: Jun 2012
Posts: 8
Default Gsva

Hi!
You could try the GSVA package in Bioconductor:
http://www.bioconductor.org/packages...html/GSVA.html

In the vignette http://www.bioconductor.org/packages...t/doc/GSVA.pdf in section 6 they explain how to use it on RNA-seq data. You do not need any DE genes. For the detection of DE gene sets they use limma from which you will obtain a p-value. They do not seem to offer one.

HTH
Ninni
ninni is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO