Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Can I test for differential expression using FPKM values? JonB Bioinformatics 7 03-05-2018 03:11 AM
Cuffdiff v2.2.1 differential expression test bug? edm1 RNA Sequencing 11 10-18-2014 04:53 AM
Any suggestion of tool for differential expression test for my situation? thejustpark RNA Sequencing 5 09-10-2014 10:40 PM
RNASeq Differential Gene Expression with two-sample Mann-Whitney test on FPKM? ndovu9 Bioinformatics 4 01-27-2014 03:58 AM
differential gene expression without replicates: edgeR, DESeq? mrfox Bioinformatics 12 05-23-2013 08:20 AM

Thread Tools
Old 06-17-2015, 01:54 AM   #1
Location: Auckland, NZ

Join Date: Nov 2011
Posts: 46
Default EdgeR test for differential expression.

I'm reading the Robinson and Smyth's 2008 paper: Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Wondering if anyone can clarify the final test being used to determine differential expression for me? The variant of fishers exact.

As I'm reading it, from section 5.2 (and from the help(exactTest()), it seems that the adjusted counts (Za and Zb) for the two conditions are added together to form another NB distribution and then it tests where in the summed distribution, the counts for Za are? That seems ... overly simple.

Is that right? Am I even looking in the right place for an explanation of how this works? Robinson et. al's 2010 edger note suggest this paper. And I can't see it clearly explained in the Zhou, Lindsay, Robinson 2014 paper either.

tirohia 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 09:44 AM.

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