SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Advice on RNA-Seq Depth KDS RNA Sequencing 3 02-19-2014 03:03 PM
Can edgeR/DESeq have more than one covariate? arrchi Bioinformatics 8 10-28-2013 02:37 PM
DESeq and edgeR papori Bioinformatics 3 05-15-2012 06:29 PM
advice/critique on my RNA-seq workflow slavailn Bioinformatics 3 12-15-2011 04:20 PM
Can DESeq and edgeR deal with in-balanced RNA-seq data? asiangg Bioinformatics 3 05-26-2010 04:45 AM

Reply
 
Thread Tools
Old 11-15-2012, 11:07 AM   #1
ugolino
Member
 
Location: maryland, usa

Join Date: Oct 2011
Posts: 14
Default advice on DESeq and EdgeR output from bacterial RNA-seq

Hi there,

I'm analyzing RNA-seq data from a bacterial monoculture exposed to 4 conditions. There are 3 bioreps for each condition and after aligning to reference using bowtie2, getting read counts with htseq (eliminated rRNA), I used both DESeq and edgeR (with TMM) to infer DE or genes. I hope the table below is clear. Column 2 and 3 are DESeq, 4 and 5 edgeR and col 6 is the overlap. FDR with BH correction, FC is fold change. EdgeR detects all the genes that DESeq detects as DE, and appreciably more. I'm really struggling to decide whether to accept only the overlap between the two, or give a chance to the genes additionally detected by edgeR. Recent literature implies slightly higher false pos rate for edgeR at n=3; on the other hand DESeq is sometimes qualified as over-conservative. But I'm no statistician, I'm a biologist and would much appreciate your insight.

thanks!

DESeq edgeR
comparison FDR 5% FC>2 FDR 5% FC>2 overlap
A:B 599 467 896 604 599
A:C 0 0 na
A 550 400 879 573 548
B:C 676 523 972 640 676
B 0 0 na
C 623 443 879 559 622


comparison of RNA-seq methods

http://www.biomedcentral.com/content...164-13-484.pdf

http://www.ncbi.nlm.nih.gov/pubmed/22988256
ugolino is offline   Reply With Quote
Old 11-15-2012, 11:10 AM   #2
ugolino
Member
 
Location: maryland, usa

Join Date: Oct 2011
Posts: 14
Default

here is the table again

DESeq edgeR
comparison FDR 5% FC>2 FDR 5% FC>2 overlap
A/B 599 467 896 604 599
A/C 0 0 na
A/D 550 400 879 573 548
B/C 676 523 972 640 676
B/D 0 0 na
C/D 623 443 879 559 622
ugolino is offline   Reply With Quote
Old 11-16-2012, 11:21 AM   #3
ugolino
Member
 
Location: maryland, usa

Join Date: Oct 2011
Posts: 14
Default

Is my post poorly formulated or simply inane? I wonder why is it being ignored?

thanks
ugolino is offline   Reply With Quote
Reply

Tags
deseq, edger, rna-seq bacterial

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 07:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO