Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
edgeR ECHo Bioinformatics 13 04-18-2013 02:01 PM
DESeq: question about with replicates and without any replicates. nb509 RNA Sequencing 2 10-25-2011 07:04 AM
edgeR p-value and logFC alessandra85 Bioinformatics 3 08-29-2011 06:04 AM
edgeR Puva Bioinformatics 2 05-19-2011 10:04 AM
edgeR and logFC MerFer Bioinformatics 0 06-29-2010 07:47 AM

Thread Tools
Old 05-02-2011, 09:51 PM   #1
Senior Member
Location: USA

Join Date: Aug 2010
Posts: 103
Default edgeR: without replicates

Hi all,
I have two RNA-Seq samples (normal and treatment) but neither has replicates. In such a case one option is to apply edgeR with Poisson model on our data. But I know that the latest edgeR can do a better job and somehow estimate the biological variation. Unfortunately, I do not know exactly how to implement this. Could anybody help me for this?

Similar questions have been discussed here:
mrfox is offline   Reply With Quote
Old 05-09-2011, 03:47 PM   #2
Gordon Smyth
Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91

Estimating biological variation without replicates is tough. edgeR offers the following solution however that will work well when the proportion of transcripts that are differentially expressed is no more than 30%. The solution is part of the new code to fit generalized linear models and to handle multi-factor experiments.

Suppose that y is your DGEList object. Setup a null design matrix with only an intercept term, then estimate the dispersion robustly from your two samples:

design0 <- matrix(1,2,1)
y <- estimateGLMCommonDisp(y,design0,method="deviance",robust=TRUE)

Then you can use the resulting dispersion estimate y$common.dispersion for your subsequent differential expression analysis.

We answer questions more regularly on the Bionconductor mailing list than on SEQanswers, so you could post questions there for more details.

Best wishes
Gordon Smyth is offline   Reply With Quote

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 11:17 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO